This is the pathway enrichment analysis practical of the OBDS course

load packages

# load librarys

library(tidyverse)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.4.0      ✔ purrr   0.3.5 
## ✔ tibble  3.1.8      ✔ dplyr   1.0.10
## ✔ tidyr   1.2.1      ✔ stringr 1.4.1 
## ✔ readr   2.1.3      ✔ forcats 0.5.2 
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
library(gprofiler2)

Read in our tables from this morning in a new Rmd file

# read in results table we output from DESeq2 this morning using tidyverse read_csv()

all_genes_df <- read.csv("~/OBDS_training/pathway_analysis/data/CD8_vs_CD4_DE_results_lfcshrinkage.csv")
dim(all_genes_df)
## [1] 22535     9
# check its dimensions - and look at the top of the file -> what does this tell us about our table? 
# dim = 22,535 -> this contains all genes -> need to filter to get those tested 

We want to perform a classic Over representation analsis (ORA) using gprofiler - to do this we first need to create our gene subsets

# Subset 1 - All genes tested in differential expression (this is our background/control gene list) - i.e. remove padj == NA 
all_genes_tested_df <- all_genes_df[!is.na(all_genes_df$padj), ]
  
dim(all_genes_tested_df)
## [1] 17729     9
# Subset 2 - All sig upregulated genes (padj < 0.05. & log2FoldChange > 1)
upreg_genes_df <- all_genes_tested_df[all_genes_tested_df$padj< 0.05 & all_genes_tested_df$log2FoldChange> 1, ]


# Subset 3 - All sig downregulated genes (padj < 0.05. & log2FoldChange < 1)
downreg_genes_df <- all_genes_tested_df[all_genes_tested_df$padj < 0.05 & all_genes_tested_df$log2FoldChange< -1, ]


# Check the dimensions of each of your dataframes using dim()
dim(downreg_genes_df)
## [1] 1204    9
dim(upreg_genes_df)
## [1] 915   9
# all_genes_df_filtered should be 17729
# upreg_genes_df should be 915
# downreg_genes_df should be 1204
# from each of these dataframes get a vector of the ensembl ids 
all_gene_ids <- all_genes_tested_df$ensembl_gene_ids
    
upreg_gene_ids <- upreg_genes_df$ensembl_gene_ids
    
downreg_gene_ids <- downreg_genes_df$ensembl_gene_ids

#Perform ORA using g:profiler

  1. Look at documentation - https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html
# use the gost() function - what parameters should we include/change??
# we want to test the ORA of upreg_gene_ids vs our all_gene_ids

# get help for function
# write query and assign to output variable named `gost_results_obj`
gost_results_obj <- gost(
  query = upreg_gene_ids,
  organism = "mmusculus",
  exclude_iea = TRUE,
  correction_method = c("g_SCS"),
  custom_bg = all_gene_ids,
  )
## Detected custom background input, domain scope is set to 'custom'
gost_results_obj$result
##       query significant      p_value term_size query_size intersection_size
## 1   query_1        TRUE 5.832954e-03         3        910                 3
## 2   query_1        TRUE 2.241023e-02         4        910                 3
## 3   query_1        TRUE 2.025637e-90      1156        910               255
## 4   query_1        TRUE 3.442480e-87      1966        910               330
## 5   query_1        TRUE 2.393765e-63       121        910                77
## 6   query_1        TRUE 2.051786e-54       367        910               116
## 7   query_1        TRUE 3.264559e-52      5351        910               508
## 8   query_1        TRUE 7.223250e-52       488        910               130
## 9   query_1        TRUE 1.041558e-51       251        910                95
## 10  query_1        TRUE 1.592447e-51       252        910                95
## 11  query_1        TRUE 1.655828e-51       258        910                96
## 12  query_1        TRUE 6.818270e-51      1064        910               193
## 13  query_1        TRUE 3.402025e-49       697        910               152
## 14  query_1        TRUE 9.610473e-49        83        910                57
## 15  query_1        TRUE 3.740459e-48        95        910                60
## 16  query_1        TRUE 4.377013e-48       393        910               113
## 17  query_1        TRUE 4.456446e-48       119        910                66
## 18  query_1        TRUE 9.691044e-48       970        910               179
## 19  query_1        TRUE 9.691044e-48       970        910               179
## 20  query_1        TRUE 2.880241e-47       539        910               131
## 21  query_1        TRUE 6.427681e-47       127        910                67
## 22  query_1        TRUE 1.170943e-46       996        910               180
## 23  query_1        TRUE 1.424216e-46      1775        910               250
## 24  query_1        TRUE 7.408844e-46      1080        910               187
## 25  query_1        TRUE 1.285341e-45       307        910                98
## 26  query_1        TRUE 1.290913e-45       834        910               162
## 27  query_1        TRUE 3.472691e-45       908        910               169
## 28  query_1        TRUE 3.598452e-45       133        910                67
## 29  query_1        TRUE 3.644339e-45        95        910                58
## 30  query_1        TRUE 1.176163e-44       219        910                83
## 31  query_1        TRUE 1.859302e-44       295        910                95
## 32  query_1        TRUE 2.071558e-44        97        910                58
## 33  query_1        TRUE 2.876977e-44       233        910                85
## 34  query_1        TRUE 2.703847e-43       481        910               119
## 35  query_1        TRUE 3.103659e-43       771        910               152
## 36  query_1        TRUE 1.535757e-42       538        910               125
## 37  query_1        TRUE 8.948207e-42       706        910               143
## 38  query_1        TRUE 4.652295e-40      1639        910               227
## 39  query_1        TRUE 6.087544e-40       558        910               124
## 40  query_1        TRUE 6.396966e-40       721        910               142
## 41  query_1        TRUE 1.349359e-39      1176        910               186
## 42  query_1        TRUE 2.105455e-39       195        910                74
## 43  query_1        TRUE 2.820957e-39       592        910               127
## 44  query_1        TRUE 3.217089e-39       245        910                82
## 45  query_1        TRUE 5.309777e-39       300        910                90
## 46  query_1        TRUE 5.744456e-39       169        910                69
## 47  query_1        TRUE 2.672814e-38       334        910                94
## 48  query_1        TRUE 2.009723e-37      3344        910               348
## 49  query_1        TRUE 3.787815e-36       489        910               111
## 50  query_1        TRUE 5.783813e-36       173        910                67
## 51  query_1        TRUE 1.000575e-35       387        910                98
## 52  query_1        TRUE 1.022499e-35       152        910                63
## 53  query_1        TRUE 1.033109e-35      1802        910               232
## 54  query_1        TRUE 1.218687e-35       169        910                66
## 55  query_1        TRUE 2.663062e-35       399        910                99
## 56  query_1        TRUE 3.592637e-35      3647        910               363
## 57  query_1        TRUE 3.925450e-35       309        910                87
## 58  query_1        TRUE 2.861754e-34      3695        910               364
## 59  query_1        TRUE 1.594773e-33       163        910                63
## 60  query_1        TRUE 6.517451e-33       351        910                90
## 61  query_1        TRUE 5.342864e-31      2803        910               296
## 62  query_1        TRUE 1.165500e-25       438        910                91
## 63  query_1        TRUE 3.830997e-23      4463        910               383
## 64  query_1        TRUE 5.684916e-23      2656        910               266
## 65  query_1        TRUE 1.317282e-22      4489        910               383
## 66  query_1        TRUE 1.688126e-19      4056        910               347
## 67  query_1        TRUE 3.688854e-16      7731        910               545
## 68  query_1        TRUE 1.319515e-14      7350        910               519
## 69  query_1        TRUE 1.999731e-13      1066        910               126
## 70  query_1        TRUE 2.685495e-13      1134        910               131
## 71  query_1        TRUE 4.862063e-13     12579        910               770
## 72  query_1        TRUE 2.395391e-12       645        910                89
## 73  query_1        TRUE 4.723526e-12      1161        910               130
## 74  query_1        TRUE 9.331910e-11       696        910                90
## 75  query_1        TRUE 1.477003e-10       471        910                70
## 76  query_1        TRUE 1.877524e-10       680        910                88
## 77  query_1        TRUE 2.070010e-10      2881        910               243
## 78  query_1        TRUE 2.491115e-10      6963        910               481
## 79  query_1        TRUE 4.816747e-10      1999        910               184
## 80  query_1        TRUE 5.578550e-10       201        910                42
## 81  query_1        TRUE 1.346141e-09       916        910               105
## 82  query_1        TRUE 2.939841e-09       347        910                56
## 83  query_1        TRUE 5.703578e-09       859        910                99
## 84  query_1        TRUE 6.391425e-09       272        910                48
## 85  query_1        TRUE 6.468373e-09      4401        910               330
## 86  query_1        TRUE 1.425667e-08       133        910                32
## 87  query_1        TRUE 1.525539e-08       158        910                35
## 88  query_1        TRUE 1.871882e-08       373        910                57
## 89  query_1        TRUE 1.871882e-08       373        910                57
## 90  query_1        TRUE 1.975494e-08      1156        910               120
## 91  query_1        TRUE 2.741647e-08       313        910                51
## 92  query_1        TRUE 4.031172e-08       163        910                35
## 93  query_1        TRUE 4.345869e-08      2296        910               197
## 94  query_1        TRUE 4.531376e-08      2718        910               224
## 95  query_1        TRUE 4.633992e-08       237        910                43
## 96  query_1        TRUE 5.236201e-08       182        910                37
## 97  query_1        TRUE 5.780609e-08       210        910                40
## 98  query_1        TRUE 6.359995e-08       220        910                41
## 99  query_1        TRUE 1.189919e-07      1805        910               163
## 100 query_1        TRUE 1.230066e-07      2697        910               221
## 101 query_1        TRUE 3.162857e-07       202        910                38
## 102 query_1        TRUE 4.590392e-07        59        910                20
## 103 query_1        TRUE 4.738735e-07        15        910                11
## 104 query_1        TRUE 4.837624e-07        12        910                10
## 105 query_1        TRUE 4.837624e-07        12        910                10
## 106 query_1        TRUE 4.837624e-07        12        910                10
## 107 query_1        TRUE 5.040220e-07       205        910                38
## 108 query_1        TRUE 6.189067e-07      1812        910               161
## 109 query_1        TRUE 6.764621e-07       798        910                89
## 110 query_1        TRUE 7.683690e-07       352        910                52
## 111 query_1        TRUE 7.776615e-07       477        910                63
## 112 query_1        TRUE 9.984716e-07       399        910                56
## 113 query_1        TRUE 1.133256e-06      3740        910               281
## 114 query_1        TRUE 1.245799e-06       768        910                86
## 115 query_1        TRUE 1.299266e-06        90        910                24
## 116 query_1        TRUE 1.303499e-06       335        910                50
## 117 query_1        TRUE 1.429006e-06      2877        910               228
## 118 query_1        TRUE 1.443889e-06        16        910                11
## 119 query_1        TRUE 1.447407e-06        98        910                25
## 120 query_1        TRUE 1.493669e-06        44        910                17
## 121 query_1        TRUE 2.384251e-06      1242        910               120
## 122 query_1        TRUE 3.084771e-06      1247        910               120
## 123 query_1        TRUE 3.765581e-06      1096        910               109
## 124 query_1        TRUE 3.857494e-06       851        910                91
## 125 query_1        TRUE 3.880582e-06      3216        910               247
## 126 query_1        TRUE 4.620974e-06      3009        910               234
## 127 query_1        TRUE 6.352809e-06       587        910                70
## 128 query_1        TRUE 6.391031e-06      2552        910               205
## 129 query_1        TRUE 8.928150e-06       579        910                69
## 130 query_1        TRUE 9.531991e-06       506        910                63
## 131 query_1        TRUE 1.099026e-05        76        910                21
## 132 query_1        TRUE 1.474430e-05       463        910                59
## 133 query_1        TRUE 1.502419e-05       229        910                38
## 134 query_1        TRUE 1.586874e-05        50        910                17
## 135 query_1        TRUE 1.713753e-05       109        910                25
## 136 query_1        TRUE 1.945984e-05       231        910                38
## 137 query_1        TRUE 2.023218e-05        71        910                20
## 138 query_1        TRUE 2.548141e-05      1994        910               167
## 139 query_1        TRUE 3.072275e-05       583        910                68
## 140 query_1        TRUE 3.371419e-05       485        910                60
## 141 query_1        TRUE 3.684121e-05        66        910                19
## 142 query_1        TRUE 4.159712e-05       105        910                24
## 143 query_1        TRUE 5.176378e-05        47        910                16
## 144 query_1        TRUE 5.935304e-05      2032        910               168
## 145 query_1        TRUE 6.274372e-05       133        910                27
## 146 query_1        TRUE 6.329281e-05      4031        910               290
## 147 query_1        TRUE 6.581978e-05       684        910                75
## 148 query_1        TRUE 6.619349e-05        61        910                18
## 149 query_1        TRUE 6.826781e-05       531        910                63
## 150 query_1        TRUE 8.383314e-05       597        910                68
## 151 query_1        TRUE 8.750879e-05      2027        910               167
## 152 query_1        TRUE 9.496596e-05       586        910                67
## 153 query_1        TRUE 1.044101e-04        85        910                21
## 154 query_1        TRUE 1.080225e-04      1190        910               111
## 155 query_1        TRUE 1.102722e-04       745        910                79
## 156 query_1        TRUE 1.240299e-04      1728        910               147
## 157 query_1        TRUE 1.313587e-04        86        910                21
## 158 query_1        TRUE 1.435816e-04        71        910                19
## 159 query_1        TRUE 1.563165e-04        64        910                18
## 160 query_1        TRUE 2.040152e-04       715        910                76
## 161 query_1        TRUE 2.415842e-04      2308        910               183
## 162 query_1        TRUE 2.497061e-04       123        910                25
## 163 query_1        TRUE 3.041920e-04      2299        910               182
## 164 query_1        TRUE 3.372744e-04       288        910                41
## 165 query_1        TRUE 3.412663e-04       223        910                35
## 166 query_1        TRUE 3.777226e-04        34        910                13
## 167 query_1        TRUE 4.796912e-04       136        910                26
## 168 query_1        TRUE 4.990232e-04        61        910                17
## 169 query_1        TRUE 5.719788e-04        35        910                13
## 170 query_1        TRUE 6.547243e-04       400        910                50
## 171 query_1        TRUE 6.567548e-04       388        910                49
## 172 query_1        TRUE 6.587471e-04        48        910                15
## 173 query_1        TRUE 7.754969e-04      1396        910               122
## 174 query_1        TRUE 8.136357e-04       130        910                25
## 175 query_1        TRUE 8.762489e-04       753        910                77
## 176 query_1        TRUE 8.919594e-04       253        910                37
## 177 query_1        TRUE 9.082526e-04       404        910                50
## 178 query_1        TRUE 9.163083e-04       392        910                49
## 179 query_1        TRUE 1.076388e-03      2483        910               191
## 180 query_1        TRUE 1.156705e-03       407        910                50
## 181 query_1        TRUE 1.206915e-03       745        910                76
## 182 query_1        TRUE 1.361077e-03       257        910                37
## 183 query_1        TRUE 1.482991e-03       338        910                44
## 184 query_1        TRUE 1.482991e-03       338        910                44
## 185 query_1        TRUE 1.655469e-03       226        910                34
## 186 query_1        TRUE 1.841379e-03         9        910                 7
## 187 query_1        TRUE 1.860759e-03        32        910                12
## 188 query_1        TRUE 1.956599e-03      3515        910               252
## 189 query_1        TRUE 2.061555e-03       700        910                72
## 190 query_1        TRUE 2.267661e-03       156        910                27
## 191 query_1        TRUE 2.294943e-03       343        910                44
## 192 query_1        TRUE 2.324280e-03       240        910                35
## 193 query_1        TRUE 2.516252e-03       263        910                37
## 194 query_1        TRUE 2.589496e-03       480        910                55
## 195 query_1        TRUE 2.654869e-03       393        910                48
## 196 query_1        TRUE 2.783988e-03        33        910                12
## 197 query_1        TRUE 3.318875e-03       722        910                73
## 198 query_1        TRUE 3.513677e-03       348        910                44
## 199 query_1        TRUE 3.535035e-03       190        910                30
## 200 query_1        TRUE 3.541536e-03       409        910                49
## 201 query_1        TRUE 3.611723e-03      1005        910                93
## 202 query_1        TRUE 3.635083e-03       397        910                48
## 203 query_1        TRUE 4.188245e-03       202        910                31
## 204 query_1        TRUE 4.469868e-03       151        910                26
## 205 query_1        TRUE 4.809657e-03       647        910                67
## 206 query_1        TRUE 4.941914e-03       634        910                66
## 207 query_1        TRUE 5.204163e-03       123        910                23
## 208 query_1        TRUE 5.204163e-03       123        910                23
## 209 query_1        TRUE 5.552641e-03       663        910                68
## 210 query_1        TRUE 5.565819e-03       543        910                59
## 211 query_1        TRUE 5.974078e-03      1045        910                95
## 212 query_1        TRUE 6.057618e-03        29        910                11
## 213 query_1        TRUE 6.600620e-03       206        910                31
## 214 query_1        TRUE 6.862475e-03       332        910                42
## 215 query_1        TRUE 7.154337e-03         7        910                 6
## 216 query_1        TRUE 7.496231e-03       419        910                49
## 217 query_1        TRUE 7.559325e-03      4379        910               299
## 218 query_1        TRUE 7.630545e-03       286        910                38
## 219 query_1        TRUE 9.419010e-03        50        910                14
## 220 query_1        TRUE 1.093351e-02       189        910                29
## 221 query_1        TRUE 1.154326e-02       759        910                74
## 222 query_1        TRUE 1.164971e-02       279        910                37
## 223 query_1        TRUE 1.200554e-02      1284        910               110
## 224 query_1        TRUE 1.232118e-02       327        910                41
## 225 query_1        TRUE 1.274683e-02        25        910                10
## 226 query_1        TRUE 1.286751e-02       110        910                21
## 227 query_1        TRUE 1.289665e-02       257        910                35
## 228 query_1        TRUE 1.404014e-02       492        910                54
## 229 query_1        TRUE 1.636075e-02       121        910                22
## 230 query_1        TRUE 1.768452e-02       431        910                49
## 231 query_1        TRUE 2.141011e-02       346        910                42
## 232 query_1        TRUE 2.481238e-02       760        910                73
## 233 query_1        TRUE 2.495971e-02        78        910                17
## 234 query_1        TRUE 2.630882e-02       186        910                28
## 235 query_1        TRUE 2.733076e-02         8        910                 6
## 236 query_1        TRUE 2.788370e-02        33        910                11
## 237 query_1        TRUE 3.115642e-02      1158        910               100
## 238 query_1        TRUE 3.494453e-02       340        910                41
## 239 query_1        TRUE 3.495387e-02        63        910                15
## 240 query_1        TRUE 3.499827e-02      1621        910               130
## 241 query_1        TRUE 3.508815e-02      1161        910               100
## 242 query_1        TRUE 3.649999e-02      1162        910               100
## 243 query_1        TRUE 4.085555e-02      1532        910               124
## 244 query_1        TRUE 4.432100e-02       368        910                43
## 245 query_1        TRUE 4.514519e-02       331        910                40
## 246 query_1        TRUE 4.534886e-02       471        910                51
## 247 query_1        TRUE 4.557239e-02       458        910                50
## 248 query_1        TRUE 4.577544e-02       688        910                67
## 249 query_1        TRUE 4.605813e-02       236        910                32
## 250 query_1        TRUE 4.668286e-02        17        910                 8
## 251 query_1        TRUE 4.945704e-02       214        910                30
## 252 query_1        TRUE 7.915622e-73       883        910               203
## 253 query_1        TRUE 1.175285e-69      1055        910               218
## 254 query_1        TRUE 3.075209e-59       408        910               127
## 255 query_1        TRUE 3.775106e-57        83        910                62
## 256 query_1        TRUE 3.521837e-54        79        910                59
## 257 query_1        TRUE 3.645920e-54      2883        910               350
## 258 query_1        TRUE 4.649234e-54      3135        910               368
## 259 query_1        TRUE 1.944937e-53       693        910               157
## 260 query_1        TRUE 1.989245e-53       576        910               143
## 261 query_1        TRUE 1.192071e-29      4591        910               409
## 262 query_1        TRUE 1.620688e-13     12523        910               769
## 263 query_1        TRUE 5.959685e-12       713        910                94
## 264 query_1        TRUE 5.995499e-11     11102        910               695
## 265 query_1        TRUE 1.189524e-10       663        910                87
## 266 query_1        TRUE 1.329217e-06       241        910                41
## 267 query_1        TRUE 2.693162e-06      1330        910               126
## 268 query_1        TRUE 1.864085e-05      1240        910               117
## 269 query_1        TRUE 2.080348e-03       741        910                75
## 270 query_1        TRUE 2.733076e-02         8        910                 6
## 271 query_1        TRUE 3.030997e-54        82        910                60
## 272 query_1        TRUE 1.023202e-49       131        910                70
## 273 query_1        TRUE 4.820958e-23       978        910               139
## 274 query_1        TRUE 3.405408e-14       475        910                77
## 275 query_1        TRUE 3.405408e-14       475        910                77
## 276 query_1        TRUE 2.440607e-13       368        910                65
## 277 query_1        TRUE 7.695264e-09        18        910                13
## 278 query_1        TRUE 7.546917e-07       103        910                26
## 279 query_1        TRUE 2.137040e-05      6386        910               426
## 280 query_1        TRUE 5.618606e-05         7        910                 7
## 281 query_1        TRUE 3.873988e-04       144        910                27
## 282 query_1        TRUE 7.154337e-03         7        910                 6
## 283 query_1        TRUE 2.036351e-02         5        910                 5
## 284 query_1        TRUE 4.977558e-02      8097        910               498
## 285 query_1        TRUE 4.536963e-08        69        910                21
## 286 query_1        TRUE 3.284042e-06        93        910                22
## 287 query_1        TRUE 7.652162e-06        97        910                22
## 288 query_1        TRUE 1.392567e-04        62        910                16
## 289 query_1        TRUE 3.792133e-03       822        910                75
## 290 query_1        TRUE 4.008578e-03       106        910                19
## 291 query_1        TRUE 5.213270e-03       311        910                37
## 292 query_1        TRUE 8.294157e-03       394        910                43
## 293 query_1        TRUE 1.221935e-02         7        910                 5
## 294 query_1        TRUE 2.048357e-02       292        910                34
## 295 query_1        TRUE 4.076467e-02       380        910                40
## 296 query_1        TRUE 4.776694e-02        94        910                16
## 297 query_1        TRUE 1.953474e-14        79        910                28
## 298 query_1        TRUE 3.514514e-09        44        910                17
## 299 query_1        TRUE 3.921882e-08        44        910                16
## 300 query_1        TRUE 1.217971e-07        47        910                16
## 301 query_1        TRUE 1.885391e-07        42        910                15
## 302 query_1        TRUE 5.637518e-07        18        910                10
## 303 query_1        TRUE 2.810751e-05        37        910                12
## 304 query_1        TRUE 2.810751e-05        37        910                12
## 305 query_1        TRUE 3.539132e-05       150        910                25
## 306 query_1        TRUE 3.922907e-05       182        910                28
## 307 query_1        TRUE 5.180607e-05        69        910                16
## 308 query_1        TRUE 5.245244e-05        61        910                15
## 309 query_1        TRUE 1.045546e-04       138        910                23
## 310 query_1        TRUE 2.052165e-04        94        910                18
## 311 query_1        TRUE 2.332183e-04        68        910                15
## 312 query_1        TRUE 2.700338e-04       115        910                20
## 313 query_1        TRUE 3.090274e-04        61        910                14
## 314 query_1        TRUE 5.969630e-04        73        910                15
## 315 query_1        TRUE 6.170792e-04        48        910                12
## 316 query_1        TRUE 6.452071e-04       153        910                23
## 317 query_1        TRUE 2.909147e-03       145        910                21
## 318 query_1        TRUE 4.429432e-03        33        910                 9
## 319 query_1        TRUE 7.754236e-03        70        910                13
## 320 query_1        TRUE 1.268988e-02       104        910                16
## 321 query_1        TRUE 1.430819e-02        30        910                 8
## 322 query_1        TRUE 2.454266e-02        99        910                15
## 323 query_1        TRUE 2.644574e-02       193        910                23
## 324 query_1        TRUE 2.663226e-02      5689        910               350
## 325 query_1        TRUE 4.556924e-02       151        910                19
## 326 query_1        TRUE 3.679020e-02        24        910                 7
## 327 query_1        TRUE 7.745029e-52        81        910                57
## 328 query_1        TRUE 1.056949e-51        78        910                56
## 329 query_1        TRUE 1.553224e-51        69        910                53
## 330 query_1        TRUE 4.622996e-51        86        910                58
## 331 query_1        TRUE 1.005040e-49        89        910                58
## 332 query_1        TRUE 1.421775e-49       148        910                72
## 333 query_1        TRUE 3.406379e-49        70        910                52
## 334 query_1        TRUE 6.939491e-49        77        910                54
## 335 query_1        TRUE 4.143923e-48        72        910                52
## 336 query_1        TRUE 8.378349e-47        85        910                55
## 337 query_1        TRUE 1.198324e-45        77        910                52
## 338 query_1        TRUE 3.608468e-45        89        910                55
## 339 query_1        TRUE 9.096294e-44        85        910                53
## 340 query_1        TRUE 1.101256e-43       157        910                69
## 341 query_1        TRUE 6.007007e-43        91        910                54
## 342 query_1        TRUE 1.311545e-42        88        910                53
## 343 query_1        TRUE 7.998747e-36       140        910                59
## 344 query_1        TRUE 3.002327e-34       121        910                54
## 345 query_1        TRUE 2.394363e-33       158        910                60
## 346 query_1        TRUE 2.916395e-31       784        910               132
## 347 query_1        TRUE 3.040915e-29       134        910                52
## 348 query_1        TRUE 1.219461e-28       463        910                95
## 349 query_1        TRUE 8.248232e-27       173        910                56
## 350 query_1        TRUE 1.366628e-25      1326        910               169
## 351 query_1        TRUE 7.788159e-21       655        910               102
## 352 query_1        TRUE 5.364922e-12       542        910                75
## 353 query_1        TRUE 4.123970e-08       120        910                27
## 354 query_1        TRUE 2.719836e-07       402        910                53
## 355 query_1        TRUE 2.826127e-07       148        910                29
## 356 query_1        TRUE 4.289012e-07         7        910                 7
## 357 query_1        TRUE 4.465165e-06      6422        910               420
## 358 query_1        TRUE 6.081574e-06       308        910                42
## 359 query_1        TRUE 4.470739e-05        10        910                 7
## 360 query_1        TRUE 4.470739e-05        10        910                 7
## 361 query_1        TRUE 6.953745e-05        30        910                11
## 362 query_1        TRUE 1.090472e-04        67        910                16
## 363 query_1        TRUE 1.191179e-04       294        910                38
## 364 query_1        TRUE 2.606949e-04        55        910                14
## 365 query_1        TRUE 2.954687e-03         4        910                 4
## 366 query_1        TRUE 4.941637e-03        44        910                11
## 367 query_1        TRUE 8.157146e-03        18        910                 7
## 368 query_1        TRUE 1.434040e-02      1609        910               121
## 369 query_1        TRUE 2.876857e-02       101        910                16
## 370 query_1        TRUE 5.778639e-07      2819        910               226
## 371 query_1        TRUE 6.534371e-05      4358        910               309
## 372 query_1        TRUE 2.318664e-03      3118        910               228
## 373 query_1        TRUE 3.062145e-03      5810        910               382
## 374 query_1        TRUE 3.588231e-03      4225        910               292
## 375 query_1        TRUE 5.943124e-03      4351        910               298
## 376 query_1        TRUE 7.144697e-03      1668        910               136
## 377 query_1        TRUE 1.405161e-02      8217        910               508
## 378 query_1        TRUE 3.469737e-07       115        910                24
## 379 query_1        TRUE 1.435710e-06        72        910                18
## 380 query_1        TRUE 6.571595e-05      3226        910               227
## 381 query_1        TRUE 2.149496e-04        39        910                11
## 382 query_1        TRUE 1.067052e-03       142        910                21
## 383 query_1        TRUE 1.515108e-03        47        910                11
## 384 query_1        TRUE 5.935056e-03        54        910                11
## 385 query_1        TRUE 2.510516e-02       152        910                19
## 386 query_1        TRUE 4.692050e-02         9        910                 4
##       precision     recall              term_id source
## 1   0.003296703 1.00000000           CORUM:2900  CORUM
## 2   0.003296703 0.75000000           CORUM:2742  CORUM
## 3   0.280219780 0.22058824           GO:0006955  GO:BP
## 4   0.362637363 0.16785351           GO:0002376  GO:BP
## 5   0.084615385 0.63636364           GO:0050853  GO:BP
## 6   0.127472527 0.31607629           GO:0002443  GO:BP
## 7   0.558241758 0.09493553           GO:0050896  GO:BP
## 8   0.142857143 0.26639344           GO:0045087  GO:BP
## 9   0.104395604 0.37848606           GO:0002429  GO:BP
## 10  0.104395604 0.37698413           GO:0002757  GO:BP
## 11  0.105494505 0.37209302           GO:0002768  GO:BP
## 12  0.212087912 0.18139098           GO:0006952  GO:BP
## 13  0.167032967 0.21807747           GO:0098542  GO:BP
## 14  0.062637363 0.68674699           GO:0006958  GO:BP
## 15  0.065934066 0.63157895           GO:0006910  GO:BP
## 16  0.124175824 0.28753181           GO:0002764  GO:BP
## 17  0.072527473 0.55462185           GO:0006911  GO:BP
## 18  0.196703297 0.18453608           GO:0043207  GO:BP
## 19  0.196703297 0.18453608           GO:0051707  GO:BP
## 20  0.143956044 0.24304267           GO:0002252  GO:BP
## 21  0.073626374 0.52755906           GO:0099024  GO:BP
## 22  0.197802198 0.18072289           GO:0009607  GO:BP
## 23  0.274725275 0.14084507           GO:0009605  GO:BP
## 24  0.205494505 0.17314815           GO:0044419  GO:BP
## 25  0.107692308 0.31921824           GO:0002253  GO:BP
## 26  0.178021978 0.19424460           GO:0045321  GO:BP
## 27  0.185714286 0.18612335           GO:0001775  GO:BP
## 28  0.073626374 0.50375940           GO:0010324  GO:BP
## 29  0.063736264 0.61052632           GO:0002455  GO:BP
## 30  0.091208791 0.37899543           GO:0050851  GO:BP
## 31  0.104395604 0.32203390           GO:0002449  GO:BP
## 32  0.063736264 0.59793814           GO:0006956  GO:BP
## 33  0.093406593 0.36480687           GO:0042742  GO:BP
## 34  0.130769231 0.24740125           GO:0050778  GO:BP
## 35  0.167032967 0.19714656           GO:0002684  GO:BP
## 36  0.137362637 0.23234201           GO:0009617  GO:BP
## 37  0.157142857 0.20254958           GO:0050776  GO:BP
## 38  0.249450549 0.13849908           GO:0048584  GO:BP
## 39  0.136263736 0.22222222           GO:0002694  GO:BP
## 40  0.156043956 0.19694868           GO:0046649  GO:BP
## 41  0.204395604 0.15816327           GO:0002682  GO:BP
## 42  0.081318681 0.37948718           GO:0050864  GO:BP
## 43  0.139560440 0.21452703           GO:0050865  GO:BP
## 44  0.090109890 0.33469388           GO:0006909  GO:BP
## 45  0.098901099 0.30000000           GO:0042113  GO:BP
## 46  0.075824176 0.40828402           GO:0006959  GO:BP
## 47  0.103296703 0.28143713           GO:0002250  GO:BP
## 48  0.382417582 0.10406699           GO:0007165  GO:BP
## 49  0.121978022 0.22699387           GO:0051249  GO:BP
## 50  0.073626374 0.38728324           GO:0019724  GO:BP
## 51  0.107692308 0.25322997           GO:0002696  GO:BP
## 52  0.069230769 0.41447368           GO:0050871  GO:BP
## 53  0.254945055 0.12874584           GO:0007166  GO:BP
## 54  0.072527473 0.39053254           GO:0016064  GO:BP
## 55  0.108791209 0.24812030           GO:0050867  GO:BP
## 56  0.398901099 0.09953386           GO:0023052  GO:BP
## 57  0.095604396 0.28155340           GO:0002460  GO:BP
## 58  0.400000000 0.09851150           GO:0007154  GO:BP
## 59  0.069230769 0.38650307           GO:0008037  GO:BP
## 60  0.098901099 0.25641026           GO:0051251  GO:BP
## 61  0.325274725 0.10560114           GO:0048583  GO:BP
## 62  0.100000000 0.20776256           GO:0006897  GO:BP
## 63  0.420879121 0.08581672           GO:0051716  GO:BP
## 64  0.292307692 0.10015060           GO:0006950  GO:BP
## 65  0.420879121 0.08531967           GO:0048518  GO:BP
## 66  0.381318681 0.08555227           GO:0048522  GO:BP
## 67  0.598901099 0.07049541           GO:0065007  GO:BP
## 68  0.570329670 0.07061224           GO:0050789  GO:BP
## 69  0.138461538 0.11819887           GO:0016477  GO:BP
## 70  0.143956044 0.11552028           GO:0016192  GO:BP
## 71  0.846153846 0.06121313           GO:0008150  GO:BP
## 72  0.097802198 0.13798450           GO:0061024  GO:BP
## 73  0.142857143 0.11197244           GO:0048870  GO:BP
## 74  0.098901099 0.12931034           GO:0032101  GO:BP
## 75  0.076923077 0.14861996           GO:0006954  GO:BP
## 76  0.096703297 0.12941176           GO:0022603  GO:BP
## 77  0.267032967 0.08434571           GO:0048731  GO:BP
## 78  0.528571429 0.06907942           GO:0050794  GO:BP
## 79  0.202197802 0.09204602           GO:0051239  GO:BP
## 80  0.046153846 0.20895522           GO:0002703  GO:BP
## 81  0.115384615 0.11462882           GO:0040011  GO:BP
## 82  0.061538462 0.16138329           GO:0032103  GO:BP
## 83  0.108791209 0.11525029           GO:0007155  GO:BP
## 84  0.052747253 0.17647059           GO:0050900  GO:BP
## 85  0.362637363 0.07498296           GO:0032501  GO:BP
## 86  0.035164835 0.24060150           GO:0001906  GO:BP
## 87  0.038461538 0.22151899           GO:0030595  GO:BP
## 88  0.062637363 0.15281501           GO:0006935  GO:BP
## 89  0.062637363 0.15281501           GO:0042330  GO:BP
## 90  0.131868132 0.10380623           GO:0051240  GO:BP
## 91  0.056043956 0.16293930           GO:0002697  GO:BP
## 92  0.038461538 0.21472393           GO:0097529  GO:BP
## 93  0.216483516 0.08580139           GO:0048513  GO:BP
## 94  0.246153846 0.08241354           GO:0048869  GO:BP
## 95  0.047252747 0.18143460           GO:0031349  GO:BP
## 96  0.040659341 0.20329670           GO:0002274  GO:BP
## 97  0.043956044 0.19047619           GO:0060326  GO:BP
## 98  0.045054945 0.18636364           GO:0002699  GO:BP
## 99  0.179120879 0.09030471           GO:0009653  GO:BP
## 100 0.242857143 0.08194290           GO:0030154  GO:BP
## 101 0.041758242 0.18811881           GO:0045765  GO:BP
## 102 0.021978022 0.33898305           GO:0043299  GO:BP
## 103 0.012087912 0.73333333           GO:0002220  GO:BP
## 104 0.010989011 0.83333333           GO:1990858  GO:BP
## 105 0.010989011 0.83333333           GO:1990840  GO:BP
## 106 0.010989011 0.83333333           GO:0002223  GO:BP
## 107 0.041758242 0.18536585           GO:1901342  GO:BP
## 108 0.176923077 0.08885210           GO:0050793  GO:BP
## 109 0.097802198 0.11152882           GO:0048534  GO:BP
## 110 0.057142857 0.14772727           GO:0007186  GO:BP
## 111 0.069230769 0.13207547           GO:0031347  GO:BP
## 112 0.061538462 0.14035088           GO:0048514  GO:BP
## 113 0.308791209 0.07513369           GO:0048856  GO:BP
## 114 0.094505495 0.11197917           GO:0030097  GO:BP
## 115 0.026373626 0.26666667           GO:0031341  GO:BP
## 116 0.054945055 0.14925373           GO:0001525  GO:BP
## 117 0.250549451 0.07924922           GO:0006810  GO:BP
## 118 0.012087912 0.68750000           GO:0002758  GO:BP
## 119 0.027472527 0.25510204           GO:0001909  GO:BP
## 120 0.018681319 0.38636364           GO:0043300  GO:BP
## 121 0.131868132 0.09661836           GO:0010647  GO:BP
## 122 0.131868132 0.09623095           GO:0023056  GO:BP
## 123 0.119780220 0.09945255           GO:0009967  GO:BP
## 124 0.100000000 0.10693302           GO:0002520  GO:BP
## 125 0.271428571 0.07680348           GO:0007275  GO:BP
## 126 0.257142857 0.07776670           GO:0051234  GO:BP
## 127 0.076923077 0.11925043           GO:0001816  GO:BP
## 128 0.225274725 0.08032915           GO:0042221  GO:BP
## 129 0.075824176 0.11917098           GO:0098609  GO:BP
## 130 0.069230769 0.12450593           GO:0002521  GO:BP
## 131 0.023076923 0.27631579           GO:0002444  GO:BP
## 132 0.064835165 0.12742981           GO:0001568  GO:BP
## 133 0.041758242 0.16593886           GO:0002366  GO:BP
## 134 0.018681319 0.34000000           GO:0002715  GO:BP
## 135 0.027472527 0.22935780           GO:0097530  GO:BP
## 136 0.041758242 0.16450216           GO:0002263  GO:BP
## 137 0.021978022 0.28169014           GO:0001910  GO:BP
## 138 0.183516484 0.08375125           GO:0010033  GO:BP
## 139 0.074725275 0.11663808           GO:0001817  GO:BP
## 140 0.065934066 0.12371134           GO:0001944  GO:BP
## 141 0.020879121 0.28787879           GO:0030593  GO:BP
## 142 0.026373626 0.22857143           GO:0034341  GO:BP
## 143 0.017582418 0.34042553           GO:0042269  GO:BP
## 144 0.184615385 0.08267717           GO:0009966  GO:BP
## 145 0.029670330 0.20300752           GO:0071674  GO:BP
## 146 0.318681319 0.07194245           GO:0032502  GO:BP
## 147 0.082417582 0.10964912           GO:0030334  GO:BP
## 148 0.019780220 0.29508197           GO:0031343  GO:BP
## 149 0.069230769 0.11864407           GO:0010942  GO:BP
## 150 0.074725275 0.11390285           GO:0030155  GO:BP
## 151 0.183516484 0.08238777           GO:0070887  GO:BP
## 152 0.073626374 0.11433447           GO:0035239  GO:BP
## 153 0.023076923 0.24705882           GO:0071621  GO:BP
## 154 0.121978022 0.09327731           GO:0042592  GO:BP
## 155 0.086813187 0.10604027           GO:0040012  GO:BP
## 156 0.161538462 0.08506944           GO:0035556  GO:BP
## 157 0.023076923 0.24418605           GO:1990266  GO:BP
## 158 0.020879121 0.26760563           GO:0002275  GO:BP
## 159 0.019780220 0.28125000           GO:0002228  GO:BP
## 160 0.083516484 0.10629371           GO:2000145  GO:BP
## 161 0.201098901 0.07928943           GO:0023051  GO:BP
## 162 0.027472527 0.20325203           GO:0002705  GO:BP
## 163 0.200000000 0.07916485           GO:0010646  GO:BP
## 164 0.045054945 0.14236111           GO:0070661  GO:BP
## 165 0.038461538 0.15695067           GO:0070663  GO:BP
## 166 0.014285714 0.38235294           GO:0002717  GO:BP
## 167 0.028571429 0.19117647           GO:0007204  GO:BP
## 168 0.018681319 0.27868852           GO:0042267  GO:BP
## 169 0.014285714 0.37142857           GO:0036230  GO:BP
## 170 0.054945055 0.12500000           GO:0098771  GO:BP
## 171 0.053846154 0.12628866           GO:0045785  GO:BP
## 172 0.016483516 0.31250000           GO:0002886  GO:BP
## 173 0.134065934 0.08739255           GO:0008283  GO:BP
## 174 0.027472527 0.19230769           GO:0019722  GO:BP
## 175 0.084615385 0.10225764           GO:0000902  GO:BP
## 176 0.040659341 0.14624506           GO:0042060  GO:BP
## 177 0.054945055 0.12376238           GO:0050801  GO:BP
## 178 0.053846154 0.12500000           GO:0055080  GO:BP
## 179 0.209890110 0.07692308           GO:0065008  GO:BP
## 180 0.054945055 0.12285012           GO:0051345  GO:BP
## 181 0.083516484 0.10201342           GO:0072359  GO:BP
## 182 0.040659341 0.14396887           GO:0046651  GO:BP
## 183 0.048351648 0.13017751           GO:0009611  GO:BP
## 184 0.048351648 0.13017751           GO:0055065  GO:BP
## 185 0.037362637 0.15044248           GO:0032496  GO:BP
## 186 0.007692308 0.77777778           GO:0010919  GO:BP
## 187 0.013186813 0.37500000           GO:0045954  GO:BP
## 188 0.276923077 0.07169275           GO:0051179  GO:BP
## 189 0.079120879 0.10285714           GO:1902533  GO:BP
## 190 0.029670330 0.17307692           GO:0002833  GO:BP
## 191 0.048351648 0.12827988           GO:0006873  GO:BP
## 192 0.038461538 0.14583333           GO:0002237  GO:BP
## 193 0.040659341 0.14068441           GO:0032943  GO:BP
## 194 0.060439560 0.11458333           GO:0043068  GO:BP
## 195 0.052747253 0.12213740           GO:0001819  GO:BP
## 196 0.013186813 0.36363636           GO:0002548  GO:BP
## 197 0.080219780 0.10110803           GO:0035295  GO:BP
## 198 0.048351648 0.12643678           GO:0030099  GO:BP
## 199 0.032967033 0.15789474           GO:0019932  GO:BP
## 200 0.053846154 0.11980440           GO:0030335  GO:BP
## 201 0.102197802 0.09253731           GO:0051094  GO:BP
## 202 0.052747253 0.12090680           GO:1903131  GO:BP
## 203 0.034065934 0.15346535           GO:0050670  GO:BP
## 204 0.028571429 0.17218543           GO:0002706  GO:BP
## 205 0.073626374 0.10355487           GO:0046903  GO:BP
## 206 0.072527473 0.10410095           GO:0051336  GO:BP
## 207 0.025274725 0.18699187           GO:0045766  GO:BP
## 208 0.025274725 0.18699187           GO:1904018  GO:BP
## 209 0.074725275 0.10256410           GO:0034097  GO:BP
## 210 0.064835165 0.10865562           GO:0000165  GO:BP
## 211 0.104395604 0.09090909           GO:2000026  GO:BP
## 212 0.012087912 0.37931034           GO:0042119  GO:BP
## 213 0.034065934 0.15048544           GO:0032944  GO:BP
## 214 0.046153846 0.12650602           GO:0030003  GO:BP
## 215 0.006593407 0.85714286           GO:0060732  GO:BP
## 216 0.053846154 0.11694511           GO:2000147  GO:BP
## 217 0.328571429 0.06828043           GO:0016043  GO:BP
## 218 0.041758242 0.13286713           GO:0002831  GO:BP
## 219 0.015384615 0.28000000           GO:0001912  GO:BP
## 220 0.031868132 0.15343915           GO:0002573  GO:BP
## 221 0.081318681 0.09749671           GO:0048646  GO:BP
## 222 0.040659341 0.13261649           GO:0006875  GO:BP
## 223 0.120879121 0.08566978           GO:0010941  GO:BP
## 224 0.045054945 0.12538226           GO:0007159  GO:BP
## 225 0.010989011 0.40000000           GO:0043302  GO:BP
## 226 0.023076923 0.19090909           GO:0050729  GO:BP
## 227 0.038461538 0.13618677           GO:0050727  GO:BP
## 228 0.059340659 0.10975610           GO:0043408  GO:BP
## 229 0.024175824 0.18181818           GO:0045089  GO:BP
## 230 0.053846154 0.11368910           GO:0040017  GO:BP
## 231 0.046153846 0.12138728           GO:0043410  GO:BP
## 232 0.080219780 0.09605263           GO:0051241  GO:BP
## 233 0.018681319 0.21794872           GO:0042100  GO:BP
## 234 0.030769231 0.15053763           GO:0045088  GO:BP
## 235 0.006593407 0.75000000           GO:0002576  GO:BP
## 236 0.012087912 0.33333333           GO:0070098  GO:BP
## 237 0.109890110 0.08635579           GO:0043067  GO:BP
## 238 0.045054945 0.12058824           GO:0002683  GO:BP
## 239 0.016483516 0.23809524           GO:0034109  GO:BP
## 240 0.142857143 0.08019741           GO:0071310  GO:BP
## 241 0.109890110 0.08613264           GO:1902531  GO:BP
## 242 0.109890110 0.08605852           GO:0042127  GO:BP
## 243 0.136263736 0.08093995           GO:0048468  GO:BP
## 244 0.047252747 0.11684783           GO:0048871  GO:BP
## 245 0.043956044 0.12084592           GO:0003013  GO:BP
## 246 0.056043956 0.10828025           GO:0043065  GO:BP
## 247 0.054945055 0.10917031           GO:0051046  GO:BP
## 248 0.073626374 0.09738372           GO:0045597  GO:BP
## 249 0.035164835 0.13559322           GO:0072507  GO:BP
## 250 0.008791209 0.47058824           GO:0002495  GO:BP
## 251 0.032967033 0.14018692           GO:0072503  GO:BP
## 252 0.223076923 0.22989807           GO:0005615  GO:CC
## 253 0.239560440 0.20663507           GO:0005576  GO:CC
## 254 0.139560440 0.31127451           GO:0009897  GO:CC
## 255 0.068131868 0.74698795           GO:0019814  GO:CC
## 256 0.064835165 0.74683544           GO:0042571  GO:CC
## 257 0.384615385 0.12140132           GO:0005886  GO:CC
## 258 0.404395604 0.11738437           GO:0071944  GO:CC
## 259 0.172527473 0.22655123           GO:0009986  GO:CC
## 260 0.157142857 0.24826389           GO:0098552  GO:CC
## 261 0.449450549 0.08908734           GO:0016020  GO:CC
## 262 0.845054945 0.06140701           GO:0005575  GO:CC
## 263 0.103296703 0.13183731           GO:0031226  GO:CC
## 264 0.763736264 0.06260133           GO:0110165  GO:CC
## 265 0.095604396 0.13122172           GO:0005887  GO:CC
## 266 0.045054945 0.17012448           GO:0043235  GO:CC
## 267 0.138461538 0.09473684           GO:0031224  GO:CC
## 268 0.128571429 0.09435484           GO:0016021  GO:CC
## 269 0.082417582 0.10121457           GO:0098590  GO:CC
## 270 0.006593407 0.75000000           GO:0042613  GO:CC
## 271 0.065934066 0.73170732           GO:0034987  GO:MF
## 272 0.076923077 0.53435115           GO:0003823  GO:MF
## 273 0.152747253 0.14212679           GO:0005102  GO:MF
## 274 0.084615385 0.16210526           GO:0060089  GO:MF
## 275 0.084615385 0.16210526           GO:0038023  GO:MF
## 276 0.071428571 0.17663043           GO:0004888  GO:MF
## 277 0.014285714 0.72222222           GO:0023023  GO:MF
## 278 0.028571429 0.25242718           GO:0140375  GO:MF
## 279 0.468131868 0.06670842           GO:0005515  GO:MF
## 280 0.007692308 1.00000000           GO:0032394  GO:MF
## 281 0.029670330 0.18750000           GO:0004930  GO:MF
## 282 0.006593407 0.85714286           GO:0023024  GO:MF
## 283 0.005494505 1.00000000           GO:0031726  GO:MF
## 284 0.547252747 0.06150426           GO:0005488  GO:MF
## 285 0.023076923 0.30434783           HP:0001287     HP
## 286 0.024175824 0.23655914           HP:0011450     HP
## 287 0.024175824 0.22680412           HP:0032158     HP
## 288 0.017582418 0.25806452           HP:0002633     HP
## 289 0.082417582 0.09124088           HP:0025142     HP
## 290 0.020879121 0.17924528           HP:0000988     HP
## 291 0.040659341 0.11897106           HP:0001945     HP
## 292 0.047252747 0.10913706           HP:0004370     HP
## 293 0.005494505 0.71428571           HP:0004444     HP
## 294 0.037362637 0.11643836           HP:0012378     HP
## 295 0.043956044 0.10526316           HP:0001744     HP
## 296 0.017582418 0.17021277           HP:0025337     HP
## 297 0.030769231 0.35443038           KEGG:04640   KEGG
## 298 0.018681319 0.38636364           KEGG:05332   KEGG
## 299 0.017582418 0.36363636           KEGG:05330   KEGG
## 300 0.017582418 0.34042553           KEGG:04940   KEGG
## 301 0.016483516 0.35714286           KEGG:05320   KEGG
## 302 0.010989011 0.55555556           KEGG:05310   KEGG
## 303 0.013186813 0.32432432           KEGG:05150   KEGG
## 304 0.013186813 0.32432432           KEGG:04672   KEGG
## 305 0.027472527 0.16666667           KEGG:04062   KEGG
## 306 0.030769231 0.15384615           KEGG:04060   KEGG
## 307 0.017582418 0.23188406           KEGG:04612   KEGG
## 308 0.016483516 0.24590164           KEGG:04061   KEGG
## 309 0.025274725 0.16666667           KEGG:04145   KEGG
## 310 0.019780220 0.19148936           KEGG:04650   KEGG
## 311 0.016483516 0.22058824           KEGG:05140   KEGG
## 312 0.021978022 0.17391304           KEGG:04514   KEGG
## 313 0.015384615 0.22950820           KEGG:05416   KEGG
## 314 0.016483516 0.20547945           KEGG:04662   KEGG
## 315 0.013186813 0.25000000           KEGG:05144   KEGG
## 316 0.025274725 0.15032680           KEGG:05152   KEGG
## 317 0.023076923 0.14482759           KEGG:05202   KEGG
## 318 0.009890110 0.27272727           KEGG:05340   KEGG
## 319 0.014285714 0.18571429           KEGG:05323   KEGG
## 320 0.017582418 0.15384615           KEGG:05145   KEGG
## 321 0.008791209 0.26666667           KEGG:05143   KEGG
## 322 0.016483516 0.15151515           KEGG:04625   KEGG
## 323 0.025274725 0.11917098           KEGG:05169   KEGG
## 324 0.384615385 0.06152224           KEGG:00000   KEGG
## 325 0.020879121 0.12582781           KEGG:04020   KEGG
## 326 0.007692308 0.29166667 MIRNA:mmu-miR-27b-3p  MIRNA
## 327 0.062637363 0.70370370   REAC:R-MMU-2168880   REAC
## 328 0.061538462 0.71794872   REAC:R-MMU-2029481   REAC
## 329 0.058241758 0.76811594   REAC:R-MMU-5690714   REAC
## 330 0.063736264 0.67441860    REAC:R-MMU-983695   REAC
## 331 0.063736264 0.65168539   REAC:R-MMU-2173782   REAC
## 332 0.079120879 0.48648649    REAC:R-MMU-198933   REAC
## 333 0.057142857 0.74285714    REAC:R-MMU-173623   REAC
## 334 0.059340659 0.70129870   REAC:R-MMU-2730905   REAC
## 335 0.057142857 0.72222222    REAC:R-MMU-166786   REAC
## 336 0.060439560 0.64705882   REAC:R-MMU-2029485   REAC
## 337 0.057142857 0.67532468    REAC:R-MMU-166663   REAC
## 338 0.060439560 0.61797753   REAC:R-MMU-2871809   REAC
## 339 0.058241758 0.62352941    REAC:R-MMU-977606   REAC
## 340 0.075824176 0.43949045    REAC:R-MMU-202733   REAC
## 341 0.059340659 0.59340659   REAC:R-MMU-2871796   REAC
## 342 0.058241758 0.60227273    REAC:R-MMU-166658   REAC
## 343 0.064835165 0.42142857   REAC:R-MMU-2029480   REAC
## 344 0.059340659 0.44628099   REAC:R-MMU-2029482   REAC
## 345 0.065934066 0.37974684    REAC:R-MMU-983705   REAC
## 346 0.145054945 0.16836735    REAC:R-MMU-168249   REAC
## 347 0.057142857 0.38805970   REAC:R-MMU-2871837   REAC
## 348 0.104395604 0.20518359    REAC:R-MMU-109582   REAC
## 349 0.061538462 0.32369942   REAC:R-MMU-2454202   REAC
## 350 0.185714286 0.12745098    REAC:R-MMU-168256   REAC
## 351 0.112087912 0.15572519   REAC:R-MMU-1280218   REAC
## 352 0.082417582 0.13837638   REAC:R-MMU-5653656   REAC
## 353 0.029670330 0.22500000    REAC:R-MMU-373076   REAC
## 354 0.058241758 0.13184080   REAC:R-MMU-6798695   REAC
## 355 0.031868132 0.19594595    REAC:R-MMU-500792   REAC
## 356 0.007692308 1.00000000   REAC:R-MMU-1247673   REAC
## 357 0.461538462 0.06540019         REAC:0000000   REAC
## 358 0.046153846 0.13636364    REAC:R-MMU-372790   REAC
## 359 0.007692308 0.70000000   REAC:R-MMU-1237044   REAC
## 360 0.007692308 0.70000000   REAC:R-MMU-1480926   REAC
## 361 0.012087912 0.36666667    REAC:R-MMU-380108   REAC
## 362 0.017582418 0.23880597    REAC:R-MMU-375276   REAC
## 363 0.041758242 0.12925170    REAC:R-MMU-388396   REAC
## 364 0.015384615 0.25454545   REAC:R-MMU-2172127   REAC
## 365 0.004395604 1.00000000   REAC:R-MMU-6799990   REAC
## 366 0.012087912 0.25000000   REAC:R-MMU-2424491   REAC
## 367 0.007692308 0.38888889   REAC:R-MMU-6803157   REAC
## 368 0.132967033 0.07520199    REAC:R-MMU-162582   REAC
## 369 0.017582418 0.15841584    REAC:R-MMU-416476   REAC
## 370 0.248351648 0.08017027            TF:M01172     TF
## 371 0.339560440 0.07090408          TF:M01808_1     TF
## 372 0.250549451 0.07312380            TF:M00658     TF
## 373 0.419780220 0.06574871            TF:M00749     TF
## 374 0.320879121 0.06911243          TF:M07107_1     TF
## 375 0.327472527 0.06849000            TF:M10270     TF
## 376 0.149450549 0.08153477          TF:M00192_1     TF
## 377 0.558241758 0.06182305            TF:M00646     TF
## 378 0.026373626 0.20869565            WP:WP1396     WP
## 379 0.019780220 0.25000000             WP:WP189     WP
## 380 0.249450549 0.07036578            WP:000000     WP
## 381 0.012087912 0.28205128            WP:WP3626     WP
## 382 0.023076923 0.14788732            WP:WP2292     WP
## 383 0.012087912 0.23404255            WP:WP3632     WP
## 384 0.012087912 0.20370370            WP:WP3625     WP
## 385 0.020879121 0.12500000              WP:WP85     WP
## 386 0.004395604 0.44444444            WP:WP2271     WP
##                                                                                                                     term_name
## 1                                                                                PLC-gamma-2-Lab-Blnk complex, BCR stimulated
## 2                                                                                                Gata2-Tal1-Tcf3-Lmo2 complex
## 3                                                                                                             immune response
## 4                                                                                                       immune system process
## 5                                                                                           B cell receptor signaling pathway
## 6                                                                                                 leukocyte mediated immunity
## 7                                                                                                        response to stimulus
## 8                                                                                                      innate immune response
## 9                                                          immune response-activating cell surface receptor signaling pathway
## 10                                                                             immune response-activating signal transduction
## 11                                                         immune response-regulating cell surface receptor signaling pathway
## 12                                                                                                           defense response
## 13                                                                                         defense response to other organism
## 14                                                                                   complement activation, classical pathway
## 15                                                                                                  phagocytosis, recognition
## 16                                                                               immune response-regulating signaling pathway
## 17                                                                                                   phagocytosis, engulfment
## 18                                                                                       response to external biotic stimulus
## 19                                                                                                 response to other organism
## 20                                                                                                    immune effector process
## 21                                                                                               plasma membrane invagination
## 22                                                                                                response to biotic stimulus
## 23                                                                                              response to external stimulus
## 24                                                  biological process involved in interspecies interaction between organisms
## 25                                                                                              activation of immune response
## 26                                                                                                       leukocyte activation
## 27                                                                                                            cell activation
## 28                                                                                                      membrane invagination
## 29                                                             humoral immune response mediated by circulating immunoglobulin
## 30                                                                                antigen receptor-mediated signaling pathway
## 31                                                                                               lymphocyte mediated immunity
## 32                                                                                                      complement activation
## 33                                                                                              defense response to bacterium
## 34                                                                                     positive regulation of immune response
## 35                                                                               positive regulation of immune system process
## 36                                                                                                      response to bacterium
## 37                                                                                              regulation of immune response
## 38                                                                                positive regulation of response to stimulus
## 39                                                                                         regulation of leukocyte activation
## 40                                                                                                      lymphocyte activation
## 41                                                                                        regulation of immune system process
## 42                                                                                            regulation of B cell activation
## 43                                                                                              regulation of cell activation
## 44                                                                                                               phagocytosis
## 45                                                                                                          B cell activation
## 46                                                                                                    humoral immune response
## 47                                                                                                   adaptive immune response
## 48                                                                                                        signal transduction
## 49                                                                                        regulation of lymphocyte activation
## 50                                                                                                   B cell mediated immunity
## 51                                                                                positive regulation of leukocyte activation
## 52                                                                                   positive regulation of B cell activation
## 53                                                                                    cell surface receptor signaling pathway
## 54                                                                                    immunoglobulin mediated immune response
## 55                                                                                     positive regulation of cell activation
## 56                                                                                                                  signaling
## 57  adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
## 58                                                                                                         cell communication
## 59                                                                                                           cell recognition
## 60                                                                               positive regulation of lymphocyte activation
## 61                                                                                         regulation of response to stimulus
## 62                                                                                                                endocytosis
## 63                                                                                              cellular response to stimulus
## 64                                                                                                         response to stress
## 65                                                                                  positive regulation of biological process
## 66                                                                                    positive regulation of cellular process
## 67                                                                                                      biological regulation
## 68                                                                                           regulation of biological process
## 69                                                                                                             cell migration
## 70                                                                                                 vesicle-mediated transport
## 71                                                                                                         biological_process
## 72                                                                                                      membrane organization
## 73                                                                                                              cell motility
## 74                                                                                regulation of response to external stimulus
## 75                                                                                                      inflammatory response
## 76                                                                           regulation of anatomical structure morphogenesis
## 77                                                                                                         system development
## 78                                                                                             regulation of cellular process
## 79                                                                             regulation of multicellular organismal process
## 80                                                                                  regulation of leukocyte mediated immunity
## 81                                                                                                                 locomotion
## 82                                                                       positive regulation of response to external stimulus
## 83                                                                                                              cell adhesion
## 84                                                                                                        leukocyte migration
## 85                                                                                           multicellular organismal process
## 86                                                                                                               cell killing
## 87                                                                                                       leukocyte chemotaxis
## 88                                                                                                                 chemotaxis
## 89                                                                                                                      taxis
## 90                                                                    positive regulation of multicellular organismal process
## 91                                                                                      regulation of immune effector process
## 92                                                                                                myeloid leukocyte migration
## 93                                                                                                   animal organ development
## 94                                                                                             cellular developmental process
## 95                                                                                    positive regulation of defense response
## 96                                                                                               myeloid leukocyte activation
## 97                                                                                                            cell chemotaxis
## 98                                                                             positive regulation of immune effector process
## 99                                                                                         anatomical structure morphogenesis
## 100                                                                                                      cell differentiation
## 101                                                                                                regulation of angiogenesis
## 102                                                                                                   leukocyte degranulation
## 103                                                 innate immune response activating cell surface receptor signaling pathway
## 104                                                                                               cellular response to lectin
## 105                                                                                                        response to lectin
## 106                                                                      stimulatory C-type lectin receptor signaling pathway
## 107                                                                                     regulation of vasculature development
## 108                                                                                       regulation of developmental process
## 109                                                                               hematopoietic or lymphoid organ development
## 110                                                                              G protein-coupled receptor signaling pathway
## 111                                                                                            regulation of defense response
## 112                                                                                                blood vessel morphogenesis
## 113                                                                                          anatomical structure development
## 114                                                                                                               hemopoiesis
## 115                                                                                                regulation of cell killing
## 116                                                                                                              angiogenesis
## 117                                                                                                                 transport
## 118                                                                     innate immune response-activating signal transduction
## 119                                                                                           leukocyte mediated cytotoxicity
## 120                                                                                     regulation of leukocyte degranulation
## 121                                                                                 positive regulation of cell communication
## 122                                                                                          positive regulation of signaling
## 123                                                                                positive regulation of signal transduction
## 124                                                                                                 immune system development
## 125                                                                                        multicellular organism development
## 126                                                                                             establishment of localization
## 127                                                                                                       cytokine production
## 128                                                                                                      response to chemical
## 129                                                                                                        cell-cell adhesion
## 130                                                                                                 leukocyte differentiation
## 131                                                                                       myeloid leukocyte mediated immunity
## 132                                                                                                  blood vessel development
## 133                                                                          leukocyte activation involved in immune response
## 134                                                                       regulation of natural killer cell mediated immunity
## 135                                                                                                     granulocyte migration
## 136                                                                               cell activation involved in immune response
## 137                                                                             regulation of leukocyte mediated cytotoxicity
## 138                                                                                             response to organic substance
## 139                                                                                         regulation of cytokine production
## 140                                                                                                   vasculature development
## 141                                                                                                     neutrophil chemotaxis
## 142                                                                                              response to interferon-gamma
## 143                                                                   regulation of natural killer cell mediated cytotoxicity
## 144                                                                                         regulation of signal transduction
## 145                                                                                                mononuclear cell migration
## 146                                                                                                     developmental process
## 147                                                                                              regulation of cell migration
## 148                                                                                       positive regulation of cell killing
## 149                                                                                         positive regulation of cell death
## 150                                                                                               regulation of cell adhesion
## 151                                                                                    cellular response to chemical stimulus
## 152                                                                                                        tube morphogenesis
## 153                                                                                                    granulocyte chemotaxis
## 154                                                                                                       homeostatic process
## 155                                                                                                  regulation of locomotion
## 156                                                                                         intracellular signal transduction
## 157                                                                                                      neutrophil migration
## 158                                                                       myeloid cell activation involved in immune response
## 159                                                                                     natural killer cell mediated immunity
## 160                                                                                               regulation of cell motility
## 161                                                                                                   regulation of signaling
## 162                                                                        positive regulation of leukocyte mediated immunity
## 163                                                                                          regulation of cell communication
## 164                                                                                                   leukocyte proliferation
## 165                                                                                     regulation of leukocyte proliferation
## 166                                                              positive regulation of natural killer cell mediated immunity
## 167                                                                positive regulation of cytosolic calcium ion concentration
## 168                                                                                 natural killer cell mediated cytotoxicity
## 169                                                                                                    granulocyte activation
## 170                                                                                                 inorganic ion homeostasis
## 171                                                                                      positive regulation of cell adhesion
## 172                                                                         regulation of myeloid leukocyte mediated immunity
## 173                                                                                             cell population proliferation
## 174                                                                                                calcium-mediated signaling
## 175                                                                                                        cell morphogenesis
## 176                                                                                                             wound healing
## 177                                                                                                           ion homeostasis
## 178                                                                                                        cation homeostasis
## 179                                                                                          regulation of biological quality
## 180                                                                                 positive regulation of hydrolase activity
## 181                                                                                            circulatory system development
## 182                                                                                                  lymphocyte proliferation
## 183                                                                                                      response to wounding
## 184                                                                                                     metal ion homeostasis
## 185                                                                                            response to lipopolysaccharide
## 186                                                                     regulation of inositol phosphate biosynthetic process
## 187                                                          positive regulation of natural killer cell mediated cytotoxicity
## 188                                                                                                              localization
## 189                                                                  positive regulation of intracellular signal transduction
## 190                                                                        positive regulation of response to biotic stimulus
## 191                                                                                                  cellular ion homeostasis
## 192                                                                                  response to molecule of bacterial origin
## 193                                                                                            mononuclear cell proliferation
## 194                                                                              positive regulation of programmed cell death
## 195                                                                                positive regulation of cytokine production
## 196                                                                                                       monocyte chemotaxis
## 197                                                                                                          tube development
## 198                                                                                              myeloid cell differentiation
## 199                                                                                       second-messenger-mediated signaling
## 200                                                                                     positive regulation of cell migration
## 201                                                                              positive regulation of developmental process
## 202                                                                                          mononuclear cell differentiation
## 203                                                                                    regulation of lymphocyte proliferation
## 204                                                                                regulation of lymphocyte mediated immunity
## 205                                                                                                                 secretion
## 206                                                                                          regulation of hydrolase activity
## 207                                                                                       positive regulation of angiogenesis
## 208                                                                            positive regulation of vasculature development
## 209                                                                                                      response to cytokine
## 210                                                                                                              MAPK cascade
## 211                                                                        regulation of multicellular organismal development
## 212                                                                                                     neutrophil activation
## 213                                                                              regulation of mononuclear cell proliferation
## 214                                                                                               cellular cation homeostasis
## 215                                                            positive regulation of inositol phosphate biosynthetic process
## 216                                                                                      positive regulation of cell motility
## 217                                                                                           cellular component organization
## 218                                                                                 regulation of response to biotic stimulus
## 219                                                                    positive regulation of leukocyte mediated cytotoxicity
## 220                                                                                         myeloid leukocyte differentiation
## 221                                                                  anatomical structure formation involved in morphogenesis
## 222                                                                                            cellular metal ion homeostasis
## 223                                                                                                  regulation of cell death
## 224                                                                                              leukocyte cell-cell adhesion
## 225                                                                            positive regulation of leukocyte degranulation
## 226                                                                              positive regulation of inflammatory response
## 227                                                                                       regulation of inflammatory response
## 228                                                                                                regulation of MAPK cascade
## 229                                                                             positive regulation of innate immune response
## 230                                                                                         positive regulation of locomotion
## 231                                                                                       positive regulation of MAPK cascade
## 232                                                                   negative regulation of multicellular organismal process
## 233                                                                                                      B cell proliferation
## 234                                                                                      regulation of innate immune response
## 235                                                                                                    platelet degranulation
## 236                                                                                      chemokine-mediated signaling pathway
## 237                                                                                       regulation of programmed cell death
## 238                                                                              negative regulation of immune system process
## 239                                                                                              homotypic cell-cell adhesion
## 240                                                                                    cellular response to organic substance
## 241                                                                           regulation of intracellular signal transduction
## 242                                                                               regulation of cell population proliferation
## 243                                                                                                          cell development
## 244                                                                                      multicellular organismal homeostasis
## 245                                                                                                circulatory system process
## 246                                                                                  positive regulation of apoptotic process
## 247                                                                                                   regulation of secretion
## 248                                                                               positive regulation of cell differentiation
## 249                                                                                     divalent inorganic cation homeostasis
## 250                                                   antigen processing and presentation of peptide antigen via MHC class II
## 251                                                                            cellular divalent inorganic cation homeostasis
## 252                                                                                                       extracellular space
## 253                                                                                                      extracellular region
## 254                                                                                          external side of plasma membrane
## 255                                                                                                    immunoglobulin complex
## 256                                                                                       immunoglobulin complex, circulating
## 257                                                                                                           plasma membrane
## 258                                                                                                            cell periphery
## 259                                                                                                              cell surface
## 260                                                                                                          side of membrane
## 261                                                                                                                  membrane
## 262                                                                                                        cellular_component
## 263                                                                                    intrinsic component of plasma membrane
## 264                                                                                                cellular anatomical entity
## 265                                                                                     integral component of plasma membrane
## 266                                                                                                          receptor complex
## 267                                                                                           intrinsic component of membrane
## 268                                                                                            integral component of membrane
## 269                                                                                                    plasma membrane region
## 270                                                                                              MHC class II protein complex
## 271                                                                                           immunoglobulin receptor binding
## 272                                                                                                           antigen binding
## 273                                                                                                signaling receptor binding
## 274                                                                                             molecular transducer activity
## 275                                                                                               signaling receptor activity
## 276                                                                                 transmembrane signaling receptor activity
## 277                                                                                               MHC protein complex binding
## 278                                                                                                  immune receptor activity
## 279                                                                                                           protein binding
## 280                                                                                            MHC class Ib receptor activity
## 281                                                                                       G protein-coupled receptor activity
## 282                                                                                       MHC class I protein complex binding
## 283                                                                                           CCR1 chemokine receptor binding
## 284                                                                                                                   binding
## 285                                                                                                                Meningitis
## 286                                                                                                     Unusual CNS infection
## 287                                                                                      Unusual infection by anatomical site
## 288                                                                                                                Vasculitis
## 289                                                                                                    Constitutional symptom
## 290                                                                                                                 Skin rash
## 291                                                                                                                     Fever
## 292                                                                                     Abnormality of temperature regulation
## 293                                                                                                             Spherocytosis
## 294                                                                                                                   Fatigue
## 295                                                                                                              Splenomegaly
## 296                                                                                                                   Red eye
## 297                                                                                                Hematopoietic cell lineage
## 298                                                                                                 Graft-versus-host disease
## 299                                                                                                       Allograft rejection
## 300                                                                                                  Type I diabetes mellitus
## 301                                                                                                Autoimmune thyroid disease
## 302                                                                                                                    Asthma
## 303                                                                                           Staphylococcus aureus infection
## 304                                                                              Intestinal immune network for IgA production
## 305                                                                                               Chemokine signaling pathway
## 306                                                                                    Cytokine-cytokine receptor interaction
## 307                                                                                       Antigen processing and presentation
## 308                                                             Viral protein interaction with cytokine and cytokine receptor
## 309                                                                                                                 Phagosome
## 310                                                                                 Natural killer cell mediated cytotoxicity
## 311                                                                                                             Leishmaniasis
## 312                                                                                                   Cell adhesion molecules
## 313                                                                                                         Viral myocarditis
## 314                                                                                         B cell receptor signaling pathway
## 315                                                                                                                   Malaria
## 316                                                                                                              Tuberculosis
## 317                                                                                   Transcriptional misregulation in cancer
## 318                                                                                                  Primary immunodeficiency
## 319                                                                                                      Rheumatoid arthritis
## 320                                                                                                             Toxoplasmosis
## 321                                                                                                   African trypanosomiasis
## 322                                                                                  C-type lectin receptor signaling pathway
## 323                                                                                              Epstein-Barr virus infection
## 324                                                                                                            KEGG root term
## 325                                                                                                 Calcium signaling pathway
## 326                                                                                                            mmu-miR-27b-3p
## 327                                                                                            Scavenging of heme from plasma
## 328                                                                                                           FCGR activation
## 329                                                                                              CD22 mediated BCR regulation
## 330                                        Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
## 331                                                                      Binding and Uptake of Ligands by Scavenger Receptors
## 332                                                  Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
## 333                                                                         Classical antibody-mediated complement activation
## 334                                                                             Role of LAT2/NTAL/LAB on calcium mobilization
## 335                                                                                          Creation of C4 and C2 activators
## 336                                                                                     Role of phospholipids in phagocytosis
## 337                                                                                          Initial triggering of complement
## 338                                                                                          FCERI mediated Ca+2 mobilization
## 339                                                                                          Regulation of Complement cascade
## 340                                                                            Cell surface interactions at the vascular wall
## 341                                                                                            FCERI mediated MAPK activation
## 342                                                                                                        Complement cascade
## 343                                                                            Fcgamma receptor (FCGR) dependent phagocytosis
## 344                                                                 Regulation of actin dynamics for phagocytic cup formation
## 345                                                                                    Signaling by the B Cell Receptor (BCR)
## 346                                                                                                      Innate Immune System
## 347                                                                                           FCERI mediated NF-kB activation
## 348                                                                                                                Hemostasis
## 349                                                                                     Fc epsilon receptor (FCERI) signaling
## 350                                                                                                             Immune System
## 351                                                                                                    Adaptive Immune System
## 352                                                                                                Vesicle-mediated transport
## 353                                                                                      Class A/1 (Rhodopsin-like receptors)
## 354                                                                                                  Neutrophil degranulation
## 355                                                                                                       GPCR ligand binding
## 356                                                                    Erythrocytes take up oxygen and release carbon dioxide
## 357                                                                                                        REACTOME root term
## 358                                                                                                         Signaling by GPCR
## 359                                                                    Erythrocytes take up carbon dioxide and release oxygen
## 360                                                                                           O2/CO2 exchange in erythrocytes
## 361                                                                                       Chemokine receptors bind chemokines
## 362                                                                                          Peptide ligand-binding receptors
## 363                                                                                                GPCR downstream signalling
## 364                                                                                                        DAP12 interactions
## 365                                                                             Metal sequestration by antimicrobial proteins
## 366                                                                                                           DAP12 signaling
## 367                                                                                                    Antimicrobial peptides
## 368                                                                                                       Signal Transduction
## 369                                                                                             G alpha (q) signalling events
## 370                                                                                  Factor: PU.1; motif: NNNNYYYACTTCCTCTTTY
## 371                                                                               Factor: NMYC; motif: CAYCTG; match class: 1
## 372                                                                                             Factor: PU.1; motif: WGAGGAAG
## 373                                                                                           Factor: SREBP-1; motif: CACSCCA
## 374                                                   Factor: LXR-alpha:RXR-alpha; motif: TGACCTNNAGTRACCYNNN; match class: 1
## 375                                                                                  Factor: IRF-4; motif: NAAARRGGAASTGARANN
## 376                                                                    Factor: GR; motif: NNNNNNCNNTNTGTNCTNN; match class: 1
## 377                                                                                            Factor: LF-A1; motif: GGGSTCWR
## 378                                                                                                       GPCRs, non-odorant 
## 379                                                                                             GPCRs, class A rhodopsin-like
## 380                                                                                                              WIKIPATHWAYS
## 381                                                                                   Microglia pathogen phagocytosis pathway
## 382                                                                                               Chemokine signaling pathway
## 383                                                                                                             Lung fibrosis
## 384                                                                                        Tyrobp causal network in microglia
## 385                                                                                                            Focal adhesion
## 386                                                                                                        Macrophage markers
##     effective_domain_size source_order
## 1                   17225          291
## 2                   17225          271
## 3                   17225         2884
## 4                   17225         1027
## 5                   17225        15352
## 6                   17225         1087
## 7                   17225        15390
## 8                   17225        13097
## 9                   17225         1073
## 10                  17225         1390
## 11                  17225         1401
## 12                  17225         2881
## 13                  17225        21964
## 14                  17225         2887
## 15                  17225         2846
## 16                  17225         1397
## 17                  17225         2847
## 18                  17225        12178
## 19                  17225        16036
## 20                  17225          905
## 21                  17225        22200
## 22                  17225         3975
## 23                  17225         3973
## 24                  17225        12763
## 25                  17225          906
## 26                  17225        13197
## 27                  17225          550
## 28                  17225         4537
## 29                  17225         1099
## 30                  17225        15350
## 31                  17225         1093
## 32                  17225         2885
## 33                  17225        11902
## 34                  17225        15295
## 35                  17225         1323
## 36                  17225         3984
## 37                  17225        15293
## 38                  17225        14876
## 39                  17225         1333
## 40                  17225        14245
## 41                  17225         1321
## 42                  17225        15363
## 43                  17225        15364
## 44                  17225         2845
## 45                  17225        11523
## 46                  17225         2888
## 47                  17225          903
## 48                  17225         3061
## 49                  17225        15684
## 50                  17225         6929
## 51                  17225         1335
## 52                  17225        15370
## 53                  17225         3062
## 54                  17225         5660
## 55                  17225        15366
## 56                  17225         7643
## 57                  17225         1104
## 58                  17225         3050
## 59                  17225         3499
## 60                  17225        15686
## 61                  17225        14875
## 62                  17225         2836
## 63                  17225        16044
## 64                  17225         2880
## 65                  17225        14820
## 66                  17225        14824
## 67                  17225        18589
## 68                  17225        15301
## 69                  17225         5812
## 70                  17225         5738
## 71                  17225         3526
## 72                  17225        17746
## 73                  17225        15139
## 74                  17225         8532
## 75                  17225         2883
## 76                  17225         7590
## 77                  17225        15011
## 78                  17225        15305
## 79                  17225        15677
## 80                  17225         1342
## 81                  17225        11442
## 82                  17225         8534
## 83                  17225         3051
## 84                  17225        15393
## 85                  17225         8794
## 86                  17225          638
## 87                  17225         7913
## 88                  17225         2869
## 89                  17225        11655
## 90                  17225        15678
## 91                  17225         1336
## 92                  17225        21844
## 93                  17225        14815
## 94                  17225        15138
## 95                  17225         8274
## 96                  17225          927
## 97                  17225        17080
## 98                  17225         1338
## 99                  17225         4017
## 100                 17225         7711
## 101                 17225        13471
## 102                 17225        12211
## 103                 17225          875
## 104                 17225        29141
## 105                 17225        29131
## 106                 17225          878
## 107                 17225        24635
## 108                 17225        15304
## 109                 17225        14834
## 110                 17225         3080
## 111                 17225         8272
## 112                 17225        14816
## 113                 17225        15126
## 114                 17225         7695
## 115                 17225         8266
## 116                 17225          435
## 117                 17225         2762
## 118                 17225         1391
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## 120                 17225        12212
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## 122                 17225         7647
## 123                 17225         4263
## 124                 17225         1163
## 125                 17225         3162
## 126                 17225        15672
## 127                 17225          583
## 128                 17225        11605
## 129                 17225        21975
## 130                 17225         1164
## 131                 17225         1088
## 132                 17225          462
## 133                 17225         1019
## 134                 17225         1354
## 135                 17225        21845
## 136                 17225          916
## 137                 17225          641
## 138                 17225         4303
## 139                 17225          584
## 140                 17225          669
## 141                 17225         7912
## 142                 17225         9844
## 143                 17225        11626
## 144                 17225         4262
## 145                 17225        19633
## 146                 17225         8795
## 147                 17225         7808
## 148                 17225         8268
## 149                 17225         5059
## 150                 17225         7712
## 151                 17225        19091
## 152                 17225        10240
## 153                 17225        19587
## 154                 17225        11816
## 155                 17225        11443
## 156                 17225        10450
## 157                 17225        28899
## 158                 17225          928
## 159                 17225          882
## 160                 17225        29352
## 161                 17225         7642
## 162                 17225         1344
## 163                 17225         4787
## 164                 17225        18970
## 165                 17225        18972
## 166                 17225         1356
## 167                 17225         3098
## 168                 17225        11624
## 169                 17225        10933
## 170                 17225        22062
## 171                 17225        13491
## 172                 17225         1518
## 173                 17225         3563
## 174                 17225         6928
## 175                 17225          307
## 176                 17225        11495
## 177                 17225        15310
## 178                 17225        16763
## 179                 17225        18590
## 180                 17225        15765
## 181                 17225        20190
## 182                 17225        14246
## 183                 17225         3979
## 184                 17225        16749
## 185                 17225         8790
## 186                 17225         5036
## 187                 17225        13640
## 188                 17225        15628
## 189                 17225        25700
## 190                 17225         1465
## 191                 17225         2812
## 192                 17225          891
## 193                 17225         9125
## 194                 17225        12108
## 195                 17225          586
## 196                 17225         1190
## 197                 17225        10274
## 198                 17225         7697
## 199                 17225         7012
## 200                 17225         7809
## 201                 17225        15551
## 202                 17225        26223
## 203                 17225        15236
## 204                 17225         1345
## 205                 17225        14421
## 206                 17225        15756
## 207                 17225        13472
## 208                 17225        27000
## 209                 17225         9659
## 210                 17225           72
## 211                 17225        29234
## 212                 17225        11527
## 213                 17225         9126
## 214                 17225         7662
## 215                 17225        17466
## 216                 17225        29354
## 217                 17225         5641
## 218                 17225         1463
## 219                 17225          643
## 220                 17225         1215
## 221                 17225        14927
## 222                 17225         2814
## 223                 17225         5058
## 224                 17225         3055
## 225                 17225        12214
## 226                 17225        15260
## 227                 17225        15258
## 228                 17225        12281
## 229                 17225        13099
## 230                 17225        11448
## 231                 17225        12283
## 232                 17225        15679
## 233                 17225        11518
## 234                 17225        13098
## 235                 17225         1218
## 236                 17225        18616
## 237                 17225        12107
## 238                 17225         1322
## 239                 17225         9668
## 240                 17225        19316
## 241                 17225        25698
## 242                 17225        11533
## 243                 17225        14785
## 244                 17225        15140
## 245                 17225         1587
## 246                 17225        12105
## 247                 17225        15517
## 248                 17225        13309
## 249                 17225        20282
## 250                 17225         1139
## 251                 17225        20278
## 252                 17225          276
## 253                 17225          239
## 254                 17225          782
## 255                 17225          969
## 256                 17225         2030
## 257                 17225          513
## 258                 17225         3125
## 259                 17225          789
## 260                 17225         3544
## 261                 17225          848
## 262                 17225          238
## 263                 17225         1236
## 264                 17225         3851
## 265                 17225          514
## 266                 17225         2128
## 267                 17225         1234
## 268                 17225          849
## 269                 17225         3576
## 270                 17225         2050
## 271                 17225         6238
## 272                 17225          513
## 273                 17225         1606
## 274                 17225         9565
## 275                 17225         6493
## 276                 17225         1435
## 277                 17225         4708
## 278                 17225        11814
## 279                 17225         1879
## 280                 17225         5365
## 281                 17225         1469
## 282                 17225         4709
## 283                 17225         5138
## 284                 17225         1862
## 285                 17225          980
## 286                 17225         7877
## 287                 17225        12203
## 288                 17225         1911
## 289                 17225         9612
## 290                 17225          773
## 291                 17225         1418
## 292                 17225         3070
## 293                 17225         3133
## 294                 17225         8791
## 295                 17225         1276
## 296                 17225         9795
## 297                 17225          317
## 298                 17225          470
## 299                 17225          469
## 300                 17225          377
## 301                 17225          465
## 302                 17225          464
## 303                 17225          422
## 304                 17225          328
## 305                 17225          240
## 306                 17225          238
## 307                 17225          306
## 308                 17225          239
## 309                 17225          266
## 310                 17225          318
## 311                 17225          416
## 312                 17225          299
## 313                 17225          476
## 314                 17225          323
## 315                 17225          419
## 316                 17225          423
## 317                 17225          437
## 318                 17225          471
## 319                 17225          468
## 320                 17225          420
## 321                 17225          418
## 322                 17225          314
## 323                 17225          433
## 324                 17225            1
## 325                 17225          235
## 326                 17225          280
## 327                 17225         1344
## 328                 17225          463
## 329                 17225          201
## 330                 17225          111
## 331                 17225          167
## 332                 17225          661
## 333                 17225          292
## 334                 17225         1297
## 335                 17225          317
## 336                 17225         1298
## 337                 17225          672
## 338                 17225          460
## 339                 17225         1219
## 340                 17225          255
## 341                 17225          461
## 342                 17225          305
## 343                 17225          495
## 344                 17225         1249
## 345                 17225         1416
## 346                 17225          674
## 347                 17225          462
## 348                 17225          628
## 349                 17225          494
## 350                 17225          660
## 351                 17225           82
## 352                 17225         1652
## 353                 17225          286
## 354                 17225          924
## 355                 17225          554
## 356                 17225          441
## 357                 17225         1711
## 358                 17225         1385
## 359                 17225          440
## 360                 17225          953
## 361                 17225          270
## 362                 17225         1017
## 363                 17225          553
## 364                 17225          335
## 365                 17225          824
## 366                 17225          336
## 367                 17225          114
## 368                 17225         1367
## 369                 17225          525
## 370                 17225         2820
## 371                 17225         2415
## 372                 17225         2822
## 373                 17225         3302
## 374                 17225         2429
## 375                 17225         1750
## 376                 17225         1407
## 377                 17225         1882
## 378                 17225           37
## 379                 17225          196
## 380                 17225            1
## 381                 17225           29
## 382                 17225          141
## 383                 17225           18
## 384                 17225          166
## 385                 17225          110
## 386                 17225          170
##                                                                    parents
## 1                                                            CORUM:0000000
## 2                                                            CORUM:0000000
## 3                                                   GO:0002376, GO:0050896
## 4                                                               GO:0008150
## 5                                                               GO:0050851
## 6                                                               GO:0002252
## 7                                                               GO:0008150
## 8                                                   GO:0006955, GO:0098542
## 9                                                   GO:0002757, GO:0002768
## 10                                                  GO:0002253, GO:0002764
## 11                                                  GO:0002764, GO:0007166
## 12                                                              GO:0006950
## 13                                                  GO:0006952, GO:0051707
## 14                                                  GO:0002455, GO:0006956
## 15                                      GO:0006897, GO:0006909, GO:0008037
## 16                                                  GO:0007165, GO:0050776
## 17                                      GO:0006897, GO:0006909, GO:0099024
## 18                                                  GO:0009605, GO:0009607
## 19                                                  GO:0043207, GO:0044419
## 20                                                              GO:0002376
## 21                                                              GO:0010324
## 22                                                              GO:0050896
## 23                                                              GO:0050896
## 24                                                              GO:0008150
## 25                                                  GO:0002376, GO:0050778
## 26                                                  GO:0001775, GO:0002376
## 27                                                              GO:0009987
## 28                                                              GO:0061024
## 29                                                  GO:0006959, GO:0016064
## 30                                                              GO:0002429
## 31                                                              GO:0002443
## 32                                      GO:0002252, GO:0002253, GO:0006959
## 33                                                  GO:0009617, GO:0098542
## 34                          GO:0002684, GO:0006955, GO:0048584, GO:0050776
## 35                                      GO:0002376, GO:0002682, GO:0048518
## 36                                                              GO:0051707
## 37                                      GO:0002682, GO:0006955, GO:0048583
## 38                                      GO:0048518, GO:0048583, GO:0050896
## 39                                      GO:0002682, GO:0045321, GO:0050865
## 40                                                              GO:0045321
## 41                                                  GO:0002376, GO:0050789
## 42                                                  GO:0042113, GO:0051249
## 43                                                  GO:0001775, GO:0050794
## 44                                                              GO:0016192
## 45                                                              GO:0046649
## 46                                                              GO:0006955
## 47                                                              GO:0006955
## 48              GO:0007154, GO:0009987, GO:0023052, GO:0050794, GO:0051716
## 49                                                  GO:0002694, GO:0046649
## 50                                                  GO:0002449, GO:0002460
## 51                          GO:0002684, GO:0002694, GO:0045321, GO:0050867
## 52                                      GO:0042113, GO:0050864, GO:0051251
## 53                                                              GO:0007165
## 54                                                              GO:0019724
## 55                                      GO:0001775, GO:0048522, GO:0050865
## 56                                                              GO:0008150
## 57                                                              GO:0002250
## 58                                                              GO:0009987
## 59                                                              GO:0009987
## 60                                      GO:0002696, GO:0046649, GO:0051249
## 61                                                  GO:0050789, GO:0050896
## 62                                                              GO:0016192
## 63                                                  GO:0009987, GO:0050896
## 64                                                              GO:0050896
## 65                                                  GO:0008150, GO:0050789
## 66                                      GO:0009987, GO:0048518, GO:0050794
## 67                                                              GO:0008150
## 68                                                  GO:0008150, GO:0065007
## 69                                                              GO:0048870
## 70                                                              GO:0006810
## 71                                                                        
## 72                                                              GO:0016043
## 73                                                              GO:0009987
## 74                                                  GO:0009605, GO:0048583
## 75                                                              GO:0006952
## 76                                                  GO:0009653, GO:0050793
## 77                                                  GO:0007275, GO:0048856
## 78                                                  GO:0009987, GO:0050789
## 79                                                  GO:0032501, GO:0050789
## 80                                                  GO:0002443, GO:0002697
## 81                                                              GO:0008150
## 82                                      GO:0009605, GO:0032101, GO:0048584
## 83                                                              GO:0009987
## 84                                                  GO:0002376, GO:0016477
## 85                                                              GO:0008150
## 86                                                              GO:0009987
## 87                                                  GO:0050900, GO:0060326
## 88                                                  GO:0042221, GO:0042330
## 89                                                  GO:0009605, GO:0040011
## 90                                      GO:0032501, GO:0048518, GO:0051239
## 91                                                  GO:0002252, GO:0002682
## 92                                                              GO:0050900
## 93                                                              GO:0048856
## 94                                                  GO:0009987, GO:0032502
## 95                                      GO:0006952, GO:0031347, GO:0048584
## 96                                                              GO:0045321
## 97                                      GO:0006935, GO:0016477, GO:0070887
## 98                                      GO:0002252, GO:0002684, GO:0002697
## 99                                                  GO:0032502, GO:0048856
## 100                                                             GO:0048869
## 101                                     GO:0001525, GO:0022603, GO:1901342
## 102                                     GO:0002252, GO:0045055, GO:0051649
## 103                                                 GO:0002429, GO:0002758
## 104                                                             GO:1990840
## 105                                                             GO:0009607
## 106                                                 GO:0002220, GO:1990858
## 107                                                 GO:0001944, GO:2000026
## 108                                                 GO:0032502, GO:0050789
## 109                                                 GO:0002520, GO:0048513
## 110                                                             GO:0007165
## 111                                                 GO:0006952, GO:0080134
## 112                                                 GO:0001568, GO:0035239
## 113                                                             GO:0032502
## 114                                                             GO:0048534
## 115                                                 GO:0001906, GO:0050794
## 116                                                 GO:0048514, GO:0048646
## 117                                                             GO:0051234
## 118                                                 GO:0002218, GO:0002757
## 119                                                 GO:0001906, GO:0002443
## 120                                     GO:0002697, GO:0043299, GO:1903305
## 121                                     GO:0007154, GO:0010646, GO:0048522
## 122                                     GO:0023051, GO:0023052, GO:0048518
## 123             GO:0007165, GO:0009966, GO:0010647, GO:0023056, GO:0048584
## 124                                                 GO:0002376, GO:0048731
## 125                                                 GO:0032501, GO:0048856
## 126                                                             GO:0051179
## 127                                                 GO:0010467, GO:0032501
## 128                                                             GO:0050896
## 129                                                             GO:0007155
## 130                                                 GO:0030097, GO:0030154
## 131                                                             GO:0002443
## 132                                                 GO:0001944, GO:0048856
## 133                                                 GO:0002263, GO:0045321
## 134                                     GO:0002228, GO:0002706, GO:0045088
## 135                                                             GO:0097529
## 136                                     GO:0001775, GO:0002252, GO:0006955
## 137                                     GO:0001909, GO:0002703, GO:0031341
## 138                                                             GO:0042221
## 139                                     GO:0001816, GO:0010468, GO:0051239
## 140                                                 GO:0048731, GO:0072359
## 141                                                 GO:0071621, GO:1990266
## 142                                                 GO:0034097, GO:0045087
## 143                                     GO:0001910, GO:0002715, GO:0042267
## 144                         GO:0007165, GO:0010646, GO:0023051, GO:0048583
## 145                                                             GO:0050900
## 146                                                             GO:0008150
## 147                                                 GO:0016477, GO:2000145
## 148                                     GO:0001906, GO:0031341, GO:0048522
## 149                                     GO:0008219, GO:0010941, GO:0048522
## 150                                                 GO:0007155, GO:0050794
## 151                                                 GO:0042221, GO:0051716
## 152                                                 GO:0009653, GO:0035295
## 153                                                 GO:0030595, GO:0097530
## 154                                                             GO:0065008
## 155                                                 GO:0040011, GO:0050789
## 156                                                             GO:0007165
## 157                                                             GO:0097530
## 158                                                 GO:0002274, GO:0002366
## 159                                                 GO:0002449, GO:0045087
## 160                                     GO:0040012, GO:0048870, GO:0050794
## 161                                                 GO:0023052, GO:0050789
## 162                                     GO:0002443, GO:0002699, GO:0002703
## 163                                                 GO:0007154, GO:0050794
## 164                                                             GO:0008283
## 165                                                 GO:0042127, GO:0070661
## 166                         GO:0002228, GO:0002708, GO:0002715, GO:0045089
## 167                                                             GO:0065008
## 168                                                 GO:0001909, GO:0002228
## 169                                                             GO:0002274
## 170                                                             GO:0050801
## 171                                     GO:0007155, GO:0030155, GO:0048522
## 172                                                 GO:0002444, GO:0002703
## 173                                                             GO:0009987
## 174                                                             GO:0019932
## 175                                                             GO:0009653
## 176                                                             GO:0009611
## 177                                                             GO:0048878
## 178                                                             GO:0050801
## 179                                                             GO:0065007
## 180                                                 GO:0043085, GO:0051336
## 181                                                             GO:0048731
## 182                                                 GO:0032943, GO:0046649
## 183                                                             GO:0006950
## 184                                                 GO:0055080, GO:0098771
## 185                                     GO:0002237, GO:0033993, GO:1901700
## 186 GO:0010675, GO:0019220, GO:0031326, GO:0032958, GO:0043255, GO:1902930
## 187                         GO:0001912, GO:0002717, GO:0042267, GO:0042269
## 188                                                             GO:0008150
## 189                                     GO:0009967, GO:0035556, GO:1902531
## 190                                     GO:0002831, GO:0009607, GO:0048584
## 191                                                 GO:0050801, GO:0055082
## 192                                     GO:0009617, GO:0010033, GO:0043207
## 193                                                             GO:0070661
## 194                                     GO:0010942, GO:0012501, GO:0043067
## 195                         GO:0001816, GO:0001817, GO:0010628, GO:0051240
## 196                                     GO:0030595, GO:0071674, GO:0097529
## 197                                                 GO:0007275, GO:0048856
## 198                                                 GO:0030097, GO:0030154
## 199                                                             GO:0035556
## 200                                     GO:0016477, GO:0030334, GO:2000147
## 201                                     GO:0032502, GO:0048518, GO:0050793
## 202                                                             GO:0002521
## 203                                     GO:0032944, GO:0046651, GO:0051249
## 204                                                 GO:0002449, GO:0002703
## 205                                                             GO:0006810
## 206                                                             GO:0050790
## 207                                     GO:0001525, GO:0045765, GO:1904018
## 208                         GO:0001944, GO:0051094, GO:0051240, GO:1901342
## 209                                                             GO:0010033
## 210                                                             GO:0035556
## 211                                     GO:0007275, GO:0050793, GO:0051239
## 212                                                             GO:0036230
## 213                                                 GO:0032943, GO:0070663
## 214                                                 GO:0006873, GO:0055080
## 215 GO:0010676, GO:0010919, GO:0031328, GO:0032958, GO:0045937, GO:1902932
## 216                         GO:0040017, GO:0048522, GO:0048870, GO:2000145
## 217                                                             GO:0071840
## 218                                                 GO:0009607, GO:0048583
## 219                         GO:0001909, GO:0001910, GO:0002705, GO:0031343
## 220                                                 GO:0002521, GO:0030099
## 221                                                 GO:0009653, GO:0032502
## 222                                                 GO:0030003, GO:0055065
## 223                                                 GO:0008219, GO:0050794
## 224                                                             GO:0098609
## 225                         GO:0002699, GO:0043299, GO:0043300, GO:1903307
## 226                         GO:0006954, GO:0031349, GO:0032103, GO:0050727
## 227                                     GO:0006954, GO:0031347, GO:0032101
## 228                                                 GO:0000165, GO:1902531
## 229 GO:0002833, GO:0031349, GO:0032103, GO:0045087, GO:0045088, GO:0050778
## 230                                     GO:0040011, GO:0040012, GO:0048518
## 231                                     GO:0000165, GO:0043408, GO:1902533
## 232                                     GO:0032501, GO:0048519, GO:0051239
## 233                                                 GO:0042113, GO:0046651
## 234             GO:0002831, GO:0031347, GO:0032101, GO:0045087, GO:0050776
## 235                                                 GO:0045055, GO:0051649
## 236                                                 GO:0019221, GO:1990869
## 237                                                 GO:0010941, GO:0012501
## 238                                     GO:0002376, GO:0002682, GO:0048519
## 239                                                             GO:0098609
## 240                                                 GO:0010033, GO:0070887
## 241                                                 GO:0009966, GO:0035556
## 242                                                 GO:0008283, GO:0050794
## 243                                     GO:0030154, GO:0048856, GO:0048869
## 244                                                 GO:0032501, GO:0042592
## 245                                                             GO:0003008
## 246                                     GO:0006915, GO:0042981, GO:0043068
## 247                                                 GO:0046903, GO:0051049
## 248                         GO:0030154, GO:0045595, GO:0048522, GO:0051094
## 249                                                 GO:0055080, GO:0098771
## 250                                                 GO:0002504, GO:0048002
## 251                                                 GO:0030003, GO:0072507
## 252                                                 GO:0005576, GO:0110165
## 253                                                             GO:0110165
## 254                                     GO:0005886, GO:0009986, GO:0098552
## 255                                                             GO:0032991
## 256                                                 GO:0005615, GO:0019814
## 257                                                 GO:0016020, GO:0071944
## 258                                                             GO:0110165
## 259                                                             GO:0110165
## 260                                                 GO:0016020, GO:0110165
## 261                                                             GO:0110165
## 262                                                                       
## 263                                                 GO:0005886, GO:0031224
## 264                                                             GO:0005575
## 265                                                 GO:0016021, GO:0031226
## 266                                                             GO:0032991
## 267                                                 GO:0016020, GO:0110165
## 268                                                             GO:0031224
## 269                                                 GO:0005886, GO:0016020
## 270                                                             GO:0042611
## 271                                                             GO:0005102
## 272                                                             GO:0005488
## 273                                                             GO:0005515
## 274                                                             GO:0003674
## 275                                                             GO:0060089
## 276                                                             GO:0038023
## 277                                                             GO:0044877
## 278                                                             GO:0038023
## 279                                                             GO:0005488
## 280                                                 GO:0004888, GO:0140375
## 281                                                             GO:0004888
## 282                                                             GO:0023023
## 283                                                             GO:0048020
## 284                                                             GO:0003674
## 285                                                             HP:0011450
## 286                                                 HP:0002011, HP:0032158
## 287                                                             HP:0032101
## 288                                                             HP:0033353
## 289                                                             HP:0000118
## 290                                                             HP:0011123
## 291                                                             HP:0004370
## 292                                                             HP:0012337
## 293                                                             HP:0004447
## 294                                                             HP:0025142
## 295                                                 HP:0003271, HP:0025408
## 296                                                             HP:0008047
## 297                                                             KEGG:00000
## 298                                                             KEGG:00000
## 299                                                             KEGG:00000
## 300                                                             KEGG:00000
## 301                                                             KEGG:00000
## 302                                                             KEGG:00000
## 303                                                             KEGG:00000
## 304                                                             KEGG:00000
## 305                                                             KEGG:00000
## 306                                                             KEGG:00000
## 307                                                             KEGG:00000
## 308                                                             KEGG:00000
## 309                                                             KEGG:00000
## 310                                                             KEGG:00000
## 311                                                             KEGG:00000
## 312                                                             KEGG:00000
## 313                                                             KEGG:00000
## 314                                                             KEGG:00000
## 315                                                             KEGG:00000
## 316                                                             KEGG:00000
## 317                                                             KEGG:00000
## 318                                                             KEGG:00000
## 319                                                             KEGG:00000
## 320                                                             KEGG:00000
## 321                                                             KEGG:00000
## 322                                                             KEGG:00000
## 323                                                             KEGG:00000
## 324                                                                       
## 325                                                             KEGG:00000
## 326                                                           MIRNA:000000
## 327                                                     REAC:R-MMU-2173782
## 328                                                     REAC:R-MMU-2029480
## 329                                                      REAC:R-MMU-983705
## 330                                                      REAC:R-MMU-983705
## 331                                                     REAC:R-MMU-5653656
## 332                                                     REAC:R-MMU-1280218
## 333                                                      REAC:R-MMU-166786
## 334                                                     REAC:R-MMU-2454202
## 335                                                      REAC:R-MMU-166663
## 336                                                     REAC:R-MMU-2029480
## 337                                                      REAC:R-MMU-166658
## 338                                                     REAC:R-MMU-2454202
## 339                                                      REAC:R-MMU-166658
## 340                                                      REAC:R-MMU-109582
## 341                                                     REAC:R-MMU-2454202
## 342                                                      REAC:R-MMU-168249
## 343                                                      REAC:R-MMU-168249
## 344                                                     REAC:R-MMU-2029480
## 345                                                     REAC:R-MMU-1280218
## 346                                                      REAC:R-MMU-168256
## 347                                                     REAC:R-MMU-2454202
## 348                                                           REAC:0000000
## 349                                                      REAC:R-MMU-168249
## 350                                                           REAC:0000000
## 351                                                      REAC:R-MMU-168256
## 352                                                           REAC:0000000
## 353                                                      REAC:R-MMU-500792
## 354                                                      REAC:R-MMU-168249
## 355                                                      REAC:R-MMU-372790
## 356                                                     REAC:R-MMU-1480926
## 357                                                                       
## 358                                                      REAC:R-MMU-162582
## 359                                                     REAC:R-MMU-1480926
## 360                                                      REAC:R-MMU-382551
## 361                                                      REAC:R-MMU-375276
## 362                                                      REAC:R-MMU-373076
## 363                                                      REAC:R-MMU-372790
## 364                                                      REAC:R-MMU-168249
## 365                                                     REAC:R-MMU-6803157
## 366                                                     REAC:R-MMU-2172127
## 367                                                      REAC:R-MMU-168249
## 368                                                           REAC:0000000
## 369                                                      REAC:R-MMU-388396
## 370                                                              TF:M00000
## 371                                                              TF:M01808
## 372                                                              TF:M00000
## 373                                                              TF:M00000
## 374                                                              TF:M07107
## 375                                                              TF:M00000
## 376                                                              TF:M00192
## 377                                                              TF:M00000
## 378                                                              WP:000000
## 379                                                              WP:000000
## 380                                                                       
## 381                                                              WP:000000
## 382                                                              WP:000000
## 383                                                              WP:000000
## 384                                                              WP:000000
## 385                                                              WP:000000
## 386                                                              WP:000000
# what are our outputs  
# plot our results using in built function in g:profiler -> which one is it? 
gostplot(
  gostres = gost_results_obj,
  capped = TRUE,
  interactive = TRUE,
  pal = c(`GO:MF` = "#dc3912", `GO:BP` = "#ff9900", `GO:CC` = "#109618", KEGG =
    "#dd4477", REAC = "#3366cc", WP = "#0099c6", TF = "#5574a6", MIRNA = "#22aa99", HPA =
    "#6633cc", CORUM = "#66aa00", HP = "#990099")
)
# what does as_short_link = FALSE do in gost() function? 
gost_results_obj_sl <- gost(
  query = upreg_gene_ids,
  organism = "mmusculus",
  exclude_iea = TRUE,
  as_short_link = TRUE,
  correction_method = c("g_SCS"),
  custom_bg = all_gene_ids,
  )
## Detected custom background input, domain scope is set to 'custom'
gost_results_obj_sl
## [1] "https://biit.cs.ut.ee/gplink/l/yb6BZAz7QW"

Answer ->

# Filter results table for genesets with between 5-300 genes 
  1. Try querying multiple gene lists at the same time (up and down regulated genes) using Multiple queries - see the documentation

Can you plot these querys together?

Output the get_version_info() to save the versions of the databases that were used for the analysis!!

Output the sessionInfo() so know what packages we used

sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] gprofiler2_0.2.1 forcats_0.5.2    stringr_1.4.1    dplyr_1.0.10    
##  [5] purrr_0.3.5      readr_2.1.3      tidyr_1.2.1      tibble_3.1.8    
##  [9] ggplot2_3.4.0    tidyverse_1.3.2 
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.4          sass_0.4.2          jsonlite_1.8.3     
##  [4] viridisLite_0.4.1   modelr_0.1.9        bslib_0.4.1        
##  [7] shiny_1.7.3         assertthat_0.2.1    googlesheets4_1.0.1
## [10] cellranger_1.1.0    yaml_2.3.6          pillar_1.8.1       
## [13] backports_1.4.1     glue_1.6.2          digest_0.6.30      
## [16] promises_1.2.0.1    rvest_1.0.3         colorspace_2.0-3   
## [19] htmltools_0.5.3     httpuv_1.6.6        pkgconfig_2.0.3    
## [22] broom_1.0.1         haven_2.5.1         xtable_1.8-4       
## [25] scales_1.2.1        later_1.3.0         tzdb_0.3.0         
## [28] timechange_0.1.1    googledrive_2.0.0   generics_0.1.3     
## [31] ellipsis_0.3.2      cachem_1.0.6        withr_2.5.0        
## [34] lazyeval_0.2.2      cli_3.4.1           magrittr_2.0.3     
## [37] crayon_1.5.2        readxl_1.4.1        mime_0.12          
## [40] evaluate_0.18       fs_1.5.2            fansi_1.0.3        
## [43] xml2_1.3.3          tools_4.2.1         data.table_1.14.4  
## [46] hms_1.1.2           gargle_1.2.1        lifecycle_1.0.3    
## [49] plotly_4.10.1       munsell_0.5.0       reprex_2.0.2       
## [52] compiler_4.2.1      jquerylib_0.1.4     rlang_1.0.6        
## [55] grid_4.2.1          RCurl_1.98-1.9      rstudioapi_0.14    
## [58] htmlwidgets_1.5.4   crosstalk_1.2.0     bitops_1.0-7       
## [61] rmarkdown_2.18      gtable_0.3.1        DBI_1.1.3          
## [64] R6_2.5.1            lubridate_1.9.0     knitr_1.40         
## [67] fastmap_1.1.0       utf8_1.2.2          stringi_1.7.8      
## [70] Rcpp_1.0.9          vctrs_0.5.0         dbplyr_2.2.1       
## [73] tidyselect_1.2.0    xfun_0.34

Now knit your report to get a lovely html file that you can share -> this is good practise as it creates a permanent record of your plots/analysis output and also makes sure your script runs without error from start to finish!